# pos

id: cord-030409-bwxkxvsl
pos: CD
token:
  1-{4-[3-Fluoro-4-((3S,6R)−3-methyl-1,1-dioxo-6-phenyl-[1,2]thiazinan-2-ylmethyl)-phenyl]-piperazin-1-yl}-ethanone

lemma:
  1-{4-[3-fluoro-4-((3s,6r)−3-methyl-1,1-dioxo-6-phenyl-[1,2]thiazinan-2-ylmethyl)-phenyl]-piperazin-1-yl}-ethanone


id: cord-275360-uphdzj5l
pos: NNP
token:
  https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergencyuse-authorizations#COVID19ivd

lemma:
  https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergencyuse-authorizations#COVID19ivd


# ent

id: cord-011444-6jh3lvm3
type: WORK_OF_ART
entity:
  Severe Acute Respiratory Syndrome SARS Multi Country Outbreak Update 47 Studies of SARS Virus Survival Situation


id: cord-003640-psnec2qp
type: ORG
entity:
  Healthy Development World Health Organization Report on Infectious Diseases Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus Role


id: cord-003640-psnec2qp
type: WORK_OF_ART
entity:
  Factors That Structure Microbial Communities A Fortran Computer Program for Permutational Multivariate Analysis


id: cord-015482-ovuofl9q
type: ORG
entity:
  Methodology Satellite Aided Survey Sampling and Implementation in Low and Middle Income Contexts A Low Cost Low Tech Alternative Openstreetmap User Generated Street Maps Using Patient Collected Clinical Samples and


id: cord-002560-pue5q5wp
type: ORG
entity:
  Astroviridae Coronaviridae Reoviridae Picornaviridae Caliciviridae Parvoviridae Adenoviridae and Papillomaviridae Families Astroviridae


id: cord-030409-bwxkxvsl
type: CHEMICAL
entity:
  1 4 3 Fluoro 4 3S 6R 3 methyl 1 1 dioxo 6 phenyl 1 2 thiazinan 2 ylmethyl phenyl piperazin 1 yl ethanone GNE


id: cord-030725-876arxiu
type: PROTEIN
entity:
  N Wymelbeke V Maitre L Sulmont Rosse C J Nutr Health Aging 2020 https doi org 10 1007 s12603 020 1388 2


id: cord-030725-876arxiu
type: GGP
entity:
  Leyderman I Yaroshetskiy A Klek S J Parenter Enteral Nutr 2020 https doi org 10 1002 jpen 1792 CLINICAL NUTRITION Evaluating the effects of dietary interventions on disease


id: cord-003523-byxuruk1
type: ORG
entity:
  Influenza C Virus and Human Metapneumovirus Infections in Hospitalized Children With Lower Respiratory Tract Illness Clinical


id: cord-290722-neqj85xf
type: CHEMICAL
entity:
  KF823811 1620 nt Phylogenetic analysis of our picobirnavirus nt sequence Fig 3 with other RdRp gene sequences of


id: cord-018761-vm86d4mj
type: WORK_OF_ART
entity:
  Guidance Note on Using the Cluster Approach to Strengthen Humanitarian Response Panel on Humanitarian Financing Report


id: cord-018761-vm86d4mj
type: EVENT
entity:
  Reference 1 World Health Organization Department of Communicable Disease Surveillance and Response Highlights


id: cord-102471-dtukacm7
type: ORG
entity:
  Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza


id: cord-103180-5hkoeca7
type: WORK_OF_ART
entity:
  Universal Screening for Acute HIV Infection in a Routine HIV Counseling and Testing Population Group Testing An Information Theory Perspective Foundations


id: cord-254596-wsmnlnlk
type: PROTEIN
entity:
  blast2rma parameters c false m 10 ms 50 me 0 01 mpi 0 top 10 supp 0 05 sup 1 alg naive mrc 0 mrefc 0 ram readCount a2t nucl_acc2tax Jul2019 abin RNA sequences


id: cord-258014-lzzi4rnz
type: ORG
entity:
  Community Ecology Package R Package Version 2 4 4 R Development Core Team R A Language and Environment for Statistical Computing R Foundation for Statistical Computing UniFrac


id: cord-298697-v1qdizwx
type: WORK_OF_ART
entity:
  ARMS Nanopore Sequencing to Expedite Barcoding of Specimen Rich Macrofaunal Samples from Autonomous Reef Monitoring Structures Front Diversity


id: cord-298697-v1qdizwx
type: WORK_OF_ART
entity:
  Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies Current Uses and


id: cord-298697-v1qdizwx
type: ORG
entity:
  NISC Comparative Sequencing Program Systematic Evaluation of Sanger Validation of Next Generation Sequencing Variants Confirming Variants


id: cord-307261-0a3iztns
type: DISEASE
entity:
  rhinovirus 4 coronavirus HKU1 2 RSV 2 adenovirus 1 Bocavirus 1 coronavirus OC43 1 and enterovirus 1 Analysis


id: cord-280846-bbv6f5gf
type: DISEASE
entity:
  influenza A H1N1 virus most closely related to swine influenza viruses We also demonstrate the utility of deep sequencing of clinical samples to identify and characterize not only the novel pathogen


id: cord-305755-6jup93v4
type: WORK_OF_ART
entity:
  A Report of 1014 Cases Chest CT for Typical 2019 nCoV Pneumonia Relationship to Negative RT PCR Testing Diagnosing


id: cord-004133-32w6g7qk
type: ORG
entity:
  Nondigital Polymerase Chain Reaction and Loop Mediated Isothermal Amplification Assays for Quantification of Human Cytomegalovirus Direct Serum Assay


id: cord-004133-32w6g7qk
type: WORK_OF_ART
entity:
  Endocervical Specimens by Polymerase Chain Reaction Genotyping Single Nucleotide Polymorphisms in Human Genomic


id: cord-004133-32w6g7qk
type: ORG
entity:
  PCR Development of a Recombinase Polymerase Amplification Assay for Detection of Epidemic Human Noroviruses


id: cord-017543-60q9iecq
type: DISEASE
entity:
  infectious agents Heightened sense for sensing recent advances in pathogen immunoassay sensing platforms Microfluidic immunosensor systems Dipstick


id: cord-345144-zvu22n8f
type: ORG
entity:
  World Health Organization WHO Commission Regulation No Military Chemical and Biological Agents Food and Agricultural Organization of the United Nations


id: cord-319685-dw0qsl4s
type: ORG
entity:
  the Histology Laboratory Veterinary Laboratory Services School of Veterinary Science and University of Liverpool


id: cord-022147-istz1iql
type: CHEMICAL
entity:
  bromophenol blue 3 0 4 6 bromocresol green 4 0 5 6 methyl red 4 4 6 0 bromocresol purple 5 0 6 6 bromothymol blue 6 0 7 6 phenol


id: cord-301991-n87le8ix
type: ORG
entity:
  the World Health Organization WHO Indian Standard Institution ISI Indian Council of Medical Research ICMR


id: cord-323973-wszo9s3d
type: ORG
entity:
  eSensor A Microarray Technology Based on Electrochemical Detection of Nucleic Acids and Its Application to Cystic Fibrosis Carrier


id: cord-344627-w2efsshj
type: TAXON
entity:
  rhinovirus human metapneumovirus human coronavirus hCoV NL63 hCoV OC43 hCoV 229E hCoV HKU 1 WU polyomavirus


id: cord-346906-1wmp43ti
type: GGP
entity:
  Nanopolish v0 11 0 35 36 and the margin_cons py script 37 https github com zibraproject zika pipeline


id: cord-345992-3ij1vbqp
type: GGP
entity:
  SARS CoV 6 7 10 11 12 Second no false positive results were allowed with the negative samples Indeterminate results in positive samples were treated as negative and in negative samples were treated as positive since the application of NAT


id: cord-345992-3ij1vbqp
type: ORG
entity:
  World Health Organization WHO SARS International Reference and Verification Laboratory Network Policy


id: cord-344131-e7phs0jd
type: PROTEIN
entity:
  cat a 23 gauge nasolacrimal cannula Figure 4 47 Topical anesthesia often is required Fill a 2 mL syringe


id: cord-344131-e7phs0jd
type: DISEASE
entity:
  renal mass lesions neoplasia renal cysts renal and ureteral traumatic lesions pyelonephritis hydroureter hydronephrosis renal agenesis hypoplasia pelvic and ureteral obstructions calculi blood clots renal parasites ectopic ureter


id: cord-017248-a37t31u1
type: CL
entity:
  stem and spinal cord Prepare frozen sections and request Sudan stain Prepare frozen sections of one half of gland and paraffin sections of the other half Petechial hemorrhages of skin chest neck and face Wounds other traumatic lesions Bone fractures Petechiae of conjunctivas and retinas Fat may accumulate on surface ofblood


id: cord-017248-a37t31u1
type: CL
entity:
  stem encephalitis Listeria monocytogenes brain stem encephalitis viral brain stem encephalitis NOTE See also under Encephalitis limbic Brain For removal and specimen preparation see Chapter 4 Necrotizing encephalitis with or without abscess formation 1 Enterocolitis Other Types or Type Undetermined NOTE A multitude of infectious and noninfectious agents


id: cord-017248-a37t31u1
type: CL
entity:
  stem and spinal cord See also above under Skull and spine and under Possible Associated Conditions Incompetence See Insufficiency Related Terms Battered child syndrome child abuse or child neglect death NOTE Vitreous should not be aspirated until the skull has been opened and trauma ruled out because there is a risk of artifactual damage to the retina In the presence of craniocerebral trauma the pathologist can opt to examine the eyes by removal fixation and histologic study or retinal photography Follow general procedures described under Homicide and if necessary the procedures described under Rape External examination See above under Note Prepare roentgenograms of entire body See above under Note In other situations or after study of the fundus submit sample of vitreous for chemical and possible toxicologic study Umbilical cord attachment Prepare histologic sections of umbilicus and end of umbilical cord Blood Submit sample for toxicologic study Consider retaining dried blood on filter paper for possible DNA


id: cord-017248-a37t31u1
type: GGP
entity:
  Reye s syndrome differential diagnosis Prevalence and non specificity of microvesicular fatty changes


id: cord-017248-a37t31u1
type: DISEASE
entity:
  infectious angiitis necrotizing arteritis polyarteritis nodosa rheumatic arteritis rheumatoid arteritis syphilitic arteritis Takayasu s arteritis


id: cord-017248-a37t31u1
type: DISEASE
entity:
  iris cataracts retinal pigmentation Ischemic lesions Artery Patent Ductal Synonym Patent ductus arteriosus


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Atrial or ventricular septal defect coarctation ofthe aorta conotruncal anomalies necrotizing enterocolitis


id: cord-017248-a37t31u1
type: DISEASE
entity:
  ventricular and atrial walls hypoplastic left atrium mitral valve left ventricle and ascending aorta mitral atresia


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Congenital biliary atresia extrahepatic biliary atresia infantile obstructive cholangio pathy syndromic Alagille s syndrome


id: cord-017248-a37t31u1
type: DISEASE
entity:
  malrotation situs inversus preduodenal portal vein absent inferior vena cava anomalous hepatic artery


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Hemosiderosis idiopathic pulmonary Lipoproteinosis pulmonary alveolar Microlithiasis pulmonary alveolar Pneumonia lipoid


id: cord-017248-a37t31u1
type: DISEASE
entity:
  acute hypersensitivity arteritis hyperthyroidism gastrointestinal hemorrhage hypothyroidism idiopathic arterial calcification


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Dreifuss mucular dystrophy facioscapulohumeral dystrophy limb girdle dystrophy myotonic muscular dystrophy


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Barre syndrome idiopathic pulmonary fibrosis idiopathic thrombocytopenic purpura IgA deficiency lichen planus


id: cord-017248-a37t31u1
type: DISEASE
entity:
  cirrhosis biliary atresia 3 Immunodeficiency See Syndrome acquired immunodeficiency and Syndrome primary immunodeficiency Impression Basilar NOTE Basilar


id: cord-017248-a37t31u1
type: DISEASE
entity:
  acquired immunodeficiency syndrome AIDS cancer cachexia inflammatory bowel disease liver or kidney failure


id: cord-017248-a37t31u1
type: DISEASE
entity:
  reflux 3 neoplasms of lungs esophagus intestine and liver chronic liver disease inflammatory bowel disease pulmonary disease


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Pharynx and gastrointestinal tract Heart liver and kidneys Record skin changes and eye abnormalities


id: cord-017248-a37t31u1
type: DISEASE
entity:
  liver and biliary tract Pulmonary Related Terms Congenital cystic adenomatoid malformation congenital pulmonary lymphangiectasis intralobular bronchopulmonary sequestration


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Collagenous inorganic dust pneumoconiosis nodular type Silicosis Noncollagenous inorganic dust pneumoconiosis


id: cord-017248-a37t31u1
type: DISEASE
entity:
  Acute lymphocytic leukemia acute myelocytic leukemia acute megakaryocytic leukemia Cardiovascular disease


id: cord-017248-a37t31u1
type: DISEASE
entity:
  atrioventricular septal defect subpulmonary stenosis pulmonary valve atresia midline symmetric liver malrotation


id: cord-017248-a37t31u1
type: DISEASE
entity:
  cerebral arteries aortic insufficiency calcific aortic stenosis coarctation of the aorta infective endocarditis Shone s syndrome Turner s syndrome


id: cord-353394-lq1f53qv
type: PROTEIN
entity:
  Clostridium difficile toxin B Clostridium perfringens Yersinia enterocolitica E coli O157 H7 enterohemorrhagic E coli stx1 2 enteropathogenic E


id: cord-353394-lq1f53qv
type: CL
entity:
  Haemophilus influenzae Chlamydophila pneumoniae Legionella pneumophila Bordetella pertussis Bordetella


id: cord-353394-lq1f53qv
type: TAXON
entity:
  adenovirus sapovirus bacterial Salmonella spp Shigella spp Vibrio spp Campylobacter spp Clostridium difficile toxin B Clostridium perfringens Yersinia


id: cord-353394-lq1f53qv
type: GGP
entity:
  HPeV 1 Fig 2 A sample collected on June 21 2016 Yangjae was positive for NoV and it had the NoV GII 17 genotype


id: cord-281916-v6u5mr2i
type: DNA
entity:
  ERV3 human endogenous retrovirus 3 Flu influenzae virus HBoV human bocavirus HCoV human coronavirus hMPV human metapneumovirus PCR polymerase chain reaction PIV paraInfluenza virus RhV EV rhino entero virus RNA ribonucleic acid ROC receiver


id: cord-354372-vfvnjmv1
type: GGP
entity:
  epidemia covid 19 riguardanti il settore funebre Emergenza covid 19 circolare ministero salute n 11285 del 1 4 2020 e ordinanza del capo dipartimento di protezione civile n


id: cord-354372-vfvnjmv1
type: FAC
entity:
  Sudden Infant Death Syndrome SIDS A Study of Cardiac Conduction System Postmortem Examination of Patients With COVID


id: cord-335372-tncjfdtp
type: ORG
entity:
  Streptococcus mutans Council on Dental Materials and Devices and Council on Dental Therapeutics Current


id: cord-342538-5bwsm290
type: DISEASE
entity:
  enteroviruses human mastadenoviruses and norovirus 16 37 38 In general for each virus a specific small fragment 400 bp of the genome


id: cord-313670-tbah33ro
type: ORG
entity:
  the Protection of Personal Data Working Document on Genetic Data Regulations European Biobank Maastricht Recommendation n R


id: cord-313670-tbah33ro
type: ORG
entity:
  the Council on Setting Standards of Quality and Safety for the Donation Procurement Testing Processing Storage and Distribution of Human Tissue Cells Caratteristiche e Modalità per la Law


id: cord-313670-tbah33ro
type: CHEMICAL
entity:
  Bioetica Europea Dir pubbl comp euro Il contratto e il corpo meritevolezza e liceità degli atti di disposizione


id: cord-294062-3esrg1jw
type: DNA
entity:
  illnessFTDFast Track DiagnosticsCtCycle thresholdHi BHaemophilus influenzae type BHi nonBnon type B Haemophilus influenzaeIQRInterquartile


id: cord-345302-wbkfjz8r
type: DNA
entity:
  families Picornaviridae 11 27 Caliciviridae 14 79 Parvoviridae 14 08 Siphoviridae 11 27 and Myoviridae 11 27 Sample VF14 92 A1


id: cord-345302-wbkfjz8r
type: ORG
entity:
  Siphoviridae Myoviridae Podoviridae Herpesviridae Reoviridae Retroviridae Polyomaviridae Inoviridae Baculoviridae


id: cord-324944-ixh3ykrc
type: GGP
entity:
  Microelectron Eng DOI 10 1016 j mee 2018 10 001 sha 2e0db82e8f0d836a489b6dfd3f101486fa05d7cc doc_id 324944 cord_uid ixh3ykrc


id: cord-324944-ixh3ykrc
type: ORG
entity:
  Informal Consultation on Fever Management in Peripheral Health Care Settings A Global Review of Evidence and Practice World Health Organization Invasive Salmonella


id: cord-324944-ixh3ykrc
type: ORG
entity:
  The WHO Working Group on Guidelines for Integrated Management of the Sick Child Integrated Management of Adolescent and Adult Illness Interim Guidelines


id: cord-324944-ixh3ykrc
type: DISEASE
entity:
  HIV 1 and HIV 2 detection within 50 min based on real time PCR with multiplexing capability 99 100 It


id: cord-317213-vhprfb1o
type: GGP
entity:
  soluble CD40 ligand sCD40L Sample size 6 μl Sample pretreatment minimal Reproducibility acceptable level of reproducibility inter assay standard derivations were 5 04 and 4 08 for hsCRP and sCD40L


id: cord-310061-nro623aa
type: PROTEIN
entity:
  cytochrome oxidase subunit 1 genes CO1 35 One PCR amplicon was selected for sequencing and compared to reference sequences


id: cord-310061-nro623aa
type: GGP
entity:
  alpha coronaviruses PREDICT_CoV 35 47 82 and 90 and three betacoronavirues PREDICT CoV 92 93 and 96 Of these the alphacoronavirus PREDICT_CoV 35


id: cord-310061-nro623aa
type: ORG
entity:
  the Ministry of Agriculture Livestock and Irrigation MOALI Ministry of Natural Resources and Environmental Conservation MONREC


id: cord-333413-8buawes0
type: PROTEIN
entity:
  J Völker I Curland N Wohlsein P Baumgärtner W Braune S Runge M Moss A Rautenschlein S Jung A Ryll M Raue K Strube C Schulz J Heffels Redmann U Fischer L Gethöffer F Voigt U Lierz M Siebert U title Health


id: cord-333413-8buawes0
type: ORG
entity:
  the Institute for Terrestrial and Aquatic Wildlife Research ITAW University of Veterinary Medicine Hannover Foundation Hannover


id: cord-333413-8buawes0
type: ORG
entity:
  the Wildlife Research Institute State Office for Nature Environment and Consumer Protection of North Rhine Westphalia


id: cord-333413-8buawes0
type: DISEASE
entity:
  bone marrow trachea thymus thyroidal gland lung heart liver pancreas spleen kidney crop proventriculus gizzard intestine adrenal gland gonads bursa of Fabricius


id: cord-023095-4dannjjm
type: PROTEIN
entity:
  SENMENGER S SYNDROME K Nakamura M Yamasaki H Ohta M Takiguchi Department of Veterinary Clinical Sciences Graduate School of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan Sildenafil


id: cord-023095-4dannjjm
type: PROTEIN
entity:
  HORSES RECEIVING ONCE DAILY GENTAMICIN JR Read 1 PA Wilkins 2 RD Nolen Walston 1 1 University of Pennsylvania New Bolton Center Kennett Square PA 2 University


id: cord-023095-4dannjjm
type: GGP
entity:
  corticotropin releasing hormone CRH adrenocorticotropin ACTH cortisol aldosterone angiotensin II ANG II arginine vasopressin AVP


id: cord-023095-4dannjjm
type: GGP
entity:
  kyphosis p 5 0 0178 degenerative joint disease p 5 0 0497 or cranial stenosis p 5 0 0357 at any site


id: cord-023095-4dannjjm
type: GGP
entity:
  lactate 1 8 3 R 2 5 0 39 and SIG 5 À0 91 Â lactate 1 0 5 R 2 5 0 41 We conclude that pH calc using SID SB tCO 2


id: cord-023095-4dannjjm
type: GGP
entity:
  cobalamin P 5 0 002 total calcium P o 0 0001 globulin P o 0 0001 cholesterol P o 0 0001 and ionized calcium P o 0


id: cord-023095-4dannjjm
type: GGP
entity:
  ENR S MDR n 5 12 or resistant ENR R MDR to enrofloxacin The minimum inhibition concentrations MICs for 11 quinolones 1


id: cord-023095-4dannjjm
type: GGP
entity:
  ENR S MDR n 5 12 The minimum inhibition concentrations MICs were determined for each isolates using broth microdilution E coli


id: cord-023095-4dannjjm
type: ORG
entity:
  Ohta M Takiguchi Department of Veterinary Clinical Sciences Graduate School of Veterinary Medicine Hokkaido University


id: cord-023095-4dannjjm
type: ORG
entity:
  The University of Tennessee College Of Veterinary Medicine s Picture Archiving and Communication System


id: cord-023095-4dannjjm
type: DISEASE
entity:
  interventricular septal wall IVS left ventricular free wall LVW left ventricular anterior wall LVAW left ventricular posterior wall LVPW


id: cord-023095-4dannjjm
type: DISEASE
entity:
  influenza A NP antibody according to manufacturer instructions The sample negative control S N absorbance


id: cord-023095-4dannjjm
type: DISEASE
entity:
  loss of appetite ocular congestion depression dehydration jaundice hematuria melena vomiting petechiae


id: cord-031907-ilhr3iu5
type: CELL_LINE
entity:
  healthy donors CytoTune iPS 2 0 Sendai Reprogramming Kit Protocol Clementino Fraga Filho UH 38583914 7 0000 5257 933 018 The EV


id: cord-031907-ilhr3iu5
type: PROTEIN
entity:
  e Phosphoglycerate Kinase 1 PGK1 Glyceraldehye 3 phosphate dehydrogenase GAPDH Aldolase ALDOA and Lactate dehydrogenase A LDHA


id: cord-031907-ilhr3iu5
type: PROTEIN
entity:
  adipocytes CD81 CD9 CD29 CD63 CD8 CD4 CD68 CD14 CD56 CD15 CD19 CD235a CD41a CD34 CD31 HLA ABC HLA G HLA DRDPDQ CD90 CD73 CD105 M Cadherin RYR1 RYR2 FABP4 DLK1


id: cord-031907-ilhr3iu5
type: PROTEIN
entity:
  tumour associated membrane receptors epidermal growth factor receptor EGFR receptor tyrosineprotein kinase ERBB2 Her2


id: cord-031907-ilhr3iu5
type: CELL_TYPE
entity:
  T cells CD4 CD8 CD25 Neutrophils GR 1 LY 6 C Dendritic cells CD11 c Macrophages CD11b MHCI MHCII NK cells CD27


id: cord-031907-ilhr3iu5
type: GGP
entity:
  Alzheimer s disease AD likely due to a progressive loss of hippocampal neurogenesis and escalation of neuroinflammation These changes are also accompanied by increased deposition of amyloid plaques


id: cord-031907-ilhr3iu5
type: GGP
entity:
  ADP p 0 01 and lower concentrations of PEVs and LEVs p 0 05 Furthermore thrombus formation was delayed p 0 003 and thrombus size was decreased p 0 008 on prostanoids Epoprostenol


id: cord-031907-ilhr3iu5
type: GGP
entity:
  Calon c Éric Boilard f and Francesca Cicchetti b a Centre de Recherche du CHU de Québec and Faculté de médecine Département de psychiatrie neurosciences Département de microbiologie infectiologie et d immunologie Evidences on microalgal extracellular vesicles


id: cord-031907-ilhr3iu5
type: PERSON
entity:
  Absara Hassan b Sonali Sharma b Jennifer Kwong b Montaha Rahman b Salma Adam b Jasmine Lee b Alvaro Villarreal Ponce


id: cord-031907-ilhr3iu5
type: ORG
entity:
  University of Pennsylvania Philadelphia USA b University of Pennsylvania philadelphia USA c Department of Bioengineering University of Pennsylvania Philadelphia USA Introduction Traumatic


id: cord-031907-ilhr3iu5
type: ORG
entity:
  Thomas Jefferson University Philadelphia USA b University of Pennsylvania School of Veterinary Medicine Philadelphia USA Introduction


id: cord-031907-ilhr3iu5
type: ORG
entity:
  Ikuhiko Nakase Department of Biological Science Graduate School of Science Osaka Prefecture University Sakai


id: cord-031907-ilhr3iu5
type: ORG
entity:
  the California Institute of Regenerative Medicine and National Institutes of Health Introduction Besides


id: cord-031907-ilhr3iu5
type: ORG
entity:
  a Laboratory of Clinical Investigation National Institutes of Ageing Baltimore USA b Department of Neurology


id: cord-031907-ilhr3iu5
type: ORG
entity:
  a Icahn School of Medicine at Mount Sinai New York USA b Mount Sinai Hospital New York USA c Department of Genetics and Genomic Sciences Department of Pathology Icahn School of Medicine Mount Sinai New York USA Introduction Diagnosis


id: cord-031907-ilhr3iu5
type: ORG
entity:
  The Brady Urological Institute Johns Hopkins University School of Medicine Baltimore USA Introduction One


id: cord-031907-ilhr3iu5
type: ORG
entity:
  a Vivex Biologics Inc Miami USA b VIVEX Biologics Inc Miami USA c VIVEX Biologics Inc Miami USA Introduction


id: cord-031907-ilhr3iu5
type: ORG
entity:
  Funding National University of Singapore R221000114114 National Medical Research Council Singapore R221000123213 Immunomodulatory


id: cord-031907-ilhr3iu5
type: ORG
entity:
  Integrative Physiology University of Nebraska Medical Center Omaha USA b Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha USA Introduction miRNAs


id: cord-031907-ilhr3iu5
type: ORG
entity:
  the National Competitiveness and Excellence Program Catalan Institution for Research and Advanced Studies


id: cord-031907-ilhr3iu5
type: LAW
entity:
  PS08 Separation and Concentration a Laboratory of Clinical Biophysics Faculty of Health Sciences PS10 Diverse EV Biomarkers Chair Pia Siljander Faculty of Biological and Environmental Sciences Urinary


id: cord-031907-ilhr3iu5
type: ORG
entity:
  Intramural Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development


id: cord-031907-ilhr3iu5
type: CHEMICAL
entity:
  phenyl R 1 3 3 4 dimethoxyphenyl 2 6 dimethylimidazo 1 2 b pyridazin 8 yl pyrrolidin 3 yl carbamate PDDC


id: cord-010119-t1x9gknd
type: CELL_LINE
entity:
  Pluripotent Stem Cell Derived Cardiomyocyte Toxicity By Supernatant of Long Term Stored Red Blood Cells


id: cord-010119-t1x9gknd
type: DNA
entity:
  RhD protein IVS1 29C rs2301153 IVS3 1 117C rs28521909 and IVS3 1 124A rs28562109 Two 15 4 were D1 and heterozygous


id: cord-010119-t1x9gknd
type: DNA
entity:
  RHD wildtype exon 9 mutant RHD c 1154G C mutant RHD c 1154 31C T and double RHD mutants c 1154G C plus c 1154 31C T


id: cord-010119-t1x9gknd
type: CELL_TYPE
entity:
  blood center RBC 2RBC PLT P PLT PLT RBC P PLT RBC 2PLT 2PLT RBC 2PLT P donations 47990 63 1775 10832 968 476 67 1150 142 10252 Citrate exposure mls 41 85 71 138 263 266 300 322 349 478 Study Design Method A randomized 2 1


id: cord-010119-t1x9gknd
type: CELL_TYPE
entity:
  ABO Rh Beckman Coulter PK System Blood Grouping and Phenotyping during the period 7 1 2008 4 1 2017 ABO


id: cord-010119-t1x9gknd
type: CELL_LINE
entity:
  Cell SaverV R HaemoneticsV R Braintree MA patients own blood shed during surgery is collected washed concentrated and reinfused lessening the need for transfusion support This study sought to examine the amount of allogeneic donor RBC


id: cord-010119-t1x9gknd
type: DNA
entity:
  ceJAL ceMO ceBI 7 0 7 0 7 0 Total 106 8 110 4 113 2 142A TRANSFUSION 2017 Vol 57 Supplement S3 reagents


id: cord-010119-t1x9gknd
type: CELL_LINE
entity:
  Immucor Gamma clone Series 4 and 5 and Quotient ALBAclone blend and alpha anti D Papain treated RBCs


id: cord-010119-t1x9gknd
type: PROTEIN
entity:
  anti Mur Brian Adkins 1 Princess Maynie 1 Carol Chandler 1 Shelia Garret 1 and Pampee Young 2 1 Vanderbilt 2


id: cord-010119-t1x9gknd
type: GGP
entity:
  gHb 7 6 6 0 3 a 5 2 6 0 3 7 3 6 0 2 a 5 5 6 0 3 7 3 6 0 4 a 4 9 6 0 5 Extracellular Lactate mM 5 6 1 a 6 6 1 7 6 0 8 6 0 6 6 0 6 6 1 Extracellular Glucose mM 32 6 1


id: cord-010119-t1x9gknd
type: GGP
entity:
  Impl periods 3 4 Table More severe reactions showed an increasing trend that only became significant in Post Impl periods 3 4


id: cord-010119-t1x9gknd
type: CL
entity:
  allogeneic blood donors and autologous donors which were intended to represent a hospitalized patient population to determine a mean and range of normal levels This 2 5 year retrospective study was performed to assess levels of RBC bound IgG IgA and IgM in normal donors Study Design Method Residual EDTA


id: cord-010119-t1x9gknd
type: ORG
entity:
  TPE Cytoreductive Therapy for Cellular Hyperviscosity Utility of Cytapheresis Treatment for Chronic Myelogenous Leukemia


id: cord-010119-t1x9gknd
type: ORG
entity:
  Washington University School of Medicine 3 Nationwide Children s Hospital Background Case Studies Transfusion


id: cord-010119-t1x9gknd
type: WORK_OF_ART
entity:
  Clinical Oral Abstract Session Novel Approaches to Processing and Assessing Cell Therapy Products A Paradigm Shift in Stem Cell Isolation and Storage Jeffrey Drew Cells4life Group LLP Background Case Studies Widespread


id: cord-010119-t1x9gknd
type: EVENT
entity:
  A Streamlined Mixed Lymphocyte Reaction MLR Assay for Evaluation of Human Mesenchymal Stem Cell Immunomodulation Activity Christopher P Delavan 1 Maryanne C Herzig 1


id: cord-010119-t1x9gknd
type: ORG
entity:
  US Army Institute of Surgical Research 2 U S Army Institute of Surgical Research Background Case Studies


id: cord-010119-t1x9gknd
type: WORK_OF_ART
entity:
  Using Genetic Markers to Select Responders and Non Responders Sickle Cell Disease SCD Patients for Transfusion with RH Haplotype Matching Red Blood


id: cord-010119-t1x9gknd
type: ORG
entity:
  Department of Pathology University of Colorado Anschutz Medical Campus 2 Department of Medicine Division of Hematology University of Colorado Hospital 3


id: cord-010119-t1x9gknd
type: ORG
entity:
  University of California San Francisco 4 Nationwide Children s Hospital 5 Academic Medical Center 6 Canadian Blood Services Background Case


id: cord-010119-t1x9gknd
type: ORG
entity:
  US Army Institute of Surgical Research 2 U S Army Institute of Surgical Research 3 University of Washington


id: cord-010119-t1x9gknd
type: ORG
entity:
  Red Cell Concentrate Volume and Manufacturing Method Impact Post Thaw Quality in Cryopreserved Products


id: cord-010119-t1x9gknd
type: ORG
entity:
  National University Hospital 3 National University Hospital Singapore Background Case Studies Plasma


id: cord-010119-t1x9gknd
type: ORG
entity:
  University of Texas Southwestern Medical Center 2 UT Southwestern Medical Center Background Case Studies


id: cord-010119-t1x9gknd
type: ORG
entity:
  mother s sisters Management of Severe Autoimmune Hemolytic Anemia A Case Report of an Infant Treated with Manual Whole Blood Exchange


id: cord-010119-t1x9gknd
type: PRODUCT
entity:
  anti e Automated Eluates Comparison of Solid Phase Red Cell Adherence and Gel Automated Eluate Testing Jayanna Slayten 1


id: cord-010119-t1x9gknd
type: ORG
entity:
  University Medical Center Department of Pathology Microbiology and Immunology Background Case Studies Antibody


id: cord-010119-t1x9gknd
type: ORG
entity:
  Graduate Institute of Clinical Medicine College of Medicine National Taiwan University 3 Division of Hepatogastroenterology Department of Internal Medicine


id: cord-010119-t1x9gknd
type: ORG
entity:
  the FDA Guidance entitled Revised Recommendations for Reducing the Risk of Zika Virus Transmission by Blood


id: cord-010119-t1x9gknd
type: ORG
entity:
  Microbiology Department Cerus Corporation 2 Scientific Affairs Department Cerus Corporation Background Case Studies


id: cord-010119-t1x9gknd
type: ORG
entity:
  Centers for Disease Control and Prevention National Health Insurance and Health Promotion Administration


id: cord-010119-t1x9gknd
type: WORK_OF_ART
entity:
  Transfusion Transmissible Infections Among Blood Donors and Strategy on Direct Laboratory Testing Cost of Blood Screening


id: cord-010119-t1x9gknd
type: ORG
entity:
  Federal State Regulations Inventory Structure Management Product Storage Testing Tracking Traceability Emergency Release Protocol


id: cord-010119-t1x9gknd
type: WORK_OF_ART
entity:
  Transfusion Service Workflow Comparison of Two High Volume High Throughput Analyzers Aaron Samson 1 Kimberly Monnin 1


id: cord-010119-t1x9gknd
type: WORK_OF_ART
entity:
  The Merging of Immunohematology Reference Lab s IRL Inventories Using Technology to Create Advanced Search


id: cord-010119-t1x9gknd
type: ORG
entity:
  Guidance for Industry Recommendations for Donor Screening Deferral and Product Management to Reduce the Risk of Transfusion Transmission of Zika Virus


id: cord-010119-t1x9gknd
type: CHEMICAL
entity:
  Cheryl Lobo 4 Michael Paul Busch 3 Susan L Stramer 2 and Jeffrey M Linnen 1 1 Grifols Diagnostic Solutions Inc 2 American Red Cross 3 Blood Systems Research Institute 4 New York Blood


id: cord-010092-uftc8inx
type: DNA
entity:
  ISBT date 2019 06 07 journal Vox Sang DOI 10 1111 vox 12792 sha 8255413c3d6cae0cd4a70c6000db8cc787837756 doc_id 10092 cord_uid uftc8inx nan


id: cord-010092-uftc8inx
type: DNA
entity:
  b globin ΤΝS9 3 55 the insulated b globin A1 TNS9 3 55and the oncogenic SFFV GFP vector Transduced cells


id: cord-010092-uftc8inx
type: PROTEIN
entity:
  heterozygous c 59T G and c 60A G p 20Leu Trp c 67A T p 23Thr Ser c 71A G and c 72G T p 24Glu Gly c 143C T s S c 208G T p 70Val Leu c 230C T p 77Thr Met


id: cord-010092-uftc8inx
type: PROTEIN
entity:
  AQP1 c 601delG CO 01N 06 mutation that induces the Co null phenotype Summary Conclusions The study provides a first overview on a number of different blood group alleles


id: cord-010092-uftc8inx
type: CL
entity:
  pRBC Summary Conclusions Atomic force microscopy in direct biophysics experiment allows to observe and to quantitatively measure the disturbances in the spectrin matrix


id: cord-010092-uftc8inx
type: CL
entity:
  allogeneic blood in breast cancer surgery is variable and differences of transfusion incidence have been observed in the literature Where the maximum surgical blood ordering schedule MSBOS dictates cross matching and reservation of blood before surgery factors deciding their utilization are varied and numerous Our hospital protocol guides that every patient planned for elective breast cancer surgery should routinely have a blood sample sent for reservation of one unit of compatible packed red blood cell


id: cord-010092-uftc8inx
type: GGP
entity:
  PFS HR 3 4 95 CI 1 9 6 3 P 0 001 for the whole study population and the TD RS subgroup HR 8 2 95 CI 3 4 21 0 P 0 001 In total 16 patients received iron chelation


id: cord-010092-uftc8inx
type: WORK_OF_ART
entity:
  HB CONTENT OF PACKED RED CELLS PRBC IS IT TIME TO LABEL EACH UNIT WITH HB CONTENT R Jain 1 N Marwaha 2 and S Sachdev 2 1 Transfusion Medicine Aiims New Delhi 2 Transfusion Medicine Pgimer Chandigarh India Background


id: cord-010092-uftc8inx
type: ORG
entity:
  N Deshpande Transfusion Medicine Tata Memorial Centre Homi Bhabha National Institute Mumbai India Background Red Blood Cell


id: cord-010092-uftc8inx
type: ORG
entity:
  Institute for Transfusion Medicine and Immunology Heidelberg University Medical Faculty Mannheim Mannheim Germany Background Rb


id: cord-010092-uftc8inx
type: ORG
entity:
  Leadership and Governance Cooperation and Collaboration Provision of Safe Blood and Blood Products Appropriate Clinical Use of Blood


id: cord-010092-uftc8inx
type: ORG
entity:
  Donor Selection Finance and Collection of Blood Bag Blood Collection Process Component Preparation Blood Testing and Blood Distribution


id: cord-010092-uftc8inx
type: EVENT
entity:
  Immunology and Transfusion Medicine Oslo University Hospital 2 Immunology University of Oslo Oslo 3 Immunology and Transfusion Medicine Akershus University


id: cord-010092-uftc8inx
type: WORK_OF_ART
entity:
  Interregional Blood Transfusion SRC Lausanne 2 Laboratory Diagnostics Interregional Blood Transfusion SRC Bern Switzerland Background


# url

id: cord-275360-uphdzj5l
domain: www.fda.gov
url:
  http://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergencyuse-authorizations#COVID19ivd


# bib

id: cord-001207-yjaiybwf
author: Sachsenröder, Jana
date: 2014-02-19
txt: ./txt/cord-001207-yjaiybwf.txt
cache: ./cache/cord-001207-yjaiybwf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929612/
doi: 10.1371/journal.pone.0088888
summary:
  faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations.

title:
  The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium

abstract:
  BACKGROUND: The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55–77%) in the samples of the youngest piglets and lowest (8–10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22–44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and “circovirus-like” viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. CONCLUSION: The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.


id: cord-002178-ggtxuulg
author: Mauk, Michael G.
date: 2015-10-20
txt: ./txt/cord-002178-ggtxuulg.txt
cache: ./cache/cord-002178-ggtxuulg.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996405/
doi: 10.3390/microarrays4040474
summary:
  A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip.

title:
  Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

abstract:
  Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 10(3) virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.


id: cord-002560-pue5q5wp
author: Moreno, Paloma S.
date: 2017-06-01
txt: ./txt/cord-002560-pue5q5wp.txt
cache: ./cache/cord-002560-pue5q5wp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453527/
doi: 10.1371/journal.pone.0178433
summary:
  Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence.

title:
  Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics

abstract:
  The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.


id: cord-003523-byxuruk1
author: Fritsch, Annemarie
date: 2019-03-07
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415498/
doi: 10.2807/1560-7917.es.2019.24.10.1800174
title:
  Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014

abstract:
  INTRODUCTION: Recent data on influenza C virus indicate a possible higher clinical impact in specified patient populations than previously thought. AIM: We aimed to investigate influenza C virus circulation in Germany. METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. The samples represented a subset of all samples from the German national surveillance system for influenza in this age group in 2012–14. The presence of influenza C virus was investigated by real-time PCR. For positive samples, information on symptoms as well as other respiratory virus co-infections was considered. Retrieved influenza C viral sequences were phylogenetically characterised. RESULTS: Influenza C viral RNA was detected in 20 (1.3% of) samples, including 16 during the 2012/13 season. The majority (18/20) of influenza C-positive patients had ILI according to the European Union definition, one patient had pneumonia. Viruses belonged to the C/Sao Paulo and C/Kanagawa lineages. Most (11/20) samples were co-infected with other respiratory viruses. CONCLUSION: Our data are the first on influenza C virus circulation in Germany and notably from a European national surveillance system. The low detection frequency and the identified virus variants confirm earlier observations outside a surveillance system. More virus detections during the 2012/13 season indicate a variable circulation intensity in the different years studied. Influenza C virus can be considered for ILI patients. Future studies addressing its clinical impact, especially in patients with severe disease are needed.


id: cord-003640-psnec2qp
title: Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment
author: Mbareche, Hamza
date: 2019-04-16
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518280/
doi: 10.3390/ijerph16081375
abstract:
  Background: Bioaerosols are a major concern for public health and sampling for exposure assessment purposes is challenging. The nasopharyngeal region could be a potent carrier of long-term bioaerosol exposure agents. This study aimed to evaluate the correlation between nasopharyngeal bacterial flora of swine workers and the swine barns bioaerosol biodiversity. Methods: Air samples from eight swine barns as well as nasopharyngeal swabs from pig workers (n = 25) and from a non-exposed control group (n = 29) were sequenced using 16S rRNA gene high-throughput sequencing. Wastewater treatment plants were used as the industrial, low-dust, non-agricultural environment control to validate the microbial link between the bioaerosol content (air) and the nasopharynxes of workers. Results: A multivariate analysis showed air samples and nasopharyngeal flora of pig workers cluster together, compared to the non-exposed control group. The significance was confirmed with the PERMANOVA statistical test (p-value of 0.0001). Unlike the farm environment, nasopharynx samples from wastewater workers did not cluster with air samples from wastewater treatment plants. The difference in the microbial community of nasopharynx of swine workers and a control group suggest that swine workers are carriers of germs found in bioaerosols. Conclusion: Nasopharynx sampling and microbiota could be used as a proxy of air sampling for exposure assessment studies or for the determination of exposure markers in highly contaminated agricultural environments.


id: cord-004133-32w6g7qk
title: Advances in Directly Amplifying Nucleic Acids from Complex Samples
author: Walker, Faye M.
date: 2019-09-30
txt: ./txt/cord-004133-32w6g7qk.txt
cache: ./cache/cord-004133-32w6g7qk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955841/
doi: 10.3390/bios9040117
summary:
  Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] .

abstract:
  Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.


id: cord-009295-4c0zwhdh
author: Bal, A.
date: 2020-03-28
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142683/
doi: 10.1016/j.cmi.2020.03.020
abstract: nan
title:
  Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)


id: cord-010092-uftc8inx
title: Abstract of 29th Regional Congress of the ISBT
author: nan
date: 2019-06-07
txt: ./txt/cord-010092-uftc8inx.txt
cache: ./cache/cord-010092-uftc8inx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/
doi: 10.1111/vox.12792
abstract: nan
summary:
  Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays.


id: cord-010119-t1x9gknd
title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017
author: nan
date: 2017-09-04
txt: ./txt/cord-010119-t1x9gknd.txt
cache: ./cache/cord-010119-t1x9gknd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/
doi: 10.1111/trf.14286
abstract: nan
summary:
  Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip).


id: cord-011444-6jh3lvm3
author: Loureiro, Natália I. V.
date: 2006-11-03
txt: ./txt/cord-011444-6jh3lvm3.txt
cache: ./cache/cord-011444-6jh3lvm3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232745/
doi: 10.1002/bmb.2004.494032060404
summary:
  These were i) avoid the use of laboratory animals that would be sacrificed; ii) the inclusion of other topics of metabolism such as glycolysis, citric acid cycle, fatty acid and amino acid synthesis and catabolism, and ketogenesis in the experimental discussion; iii) the experiment should have low cost and be performed after the relevant theory material is studied; and finally iv) it also should be easy and fast, due to the limited time of the practical class. In this article, we will present the protocol and approach used in this practice class, also including the evaluation by student teaching assistants and undergraduate students from nine different courses ("Biological Science," "Pharmacy," "Medicine," "Veterinary Medicine," "Nutrition," "Nursing," "Odontology," "Chemistry," and "Industrial Chemistry"). After the preparation of the protocol and arranging all necessary laboratory material including the guarurine, it was possible to evaluate this new practical class with the group of student teaching assistants from the Biochemistry discipline (n ϭ 6).

title:
  Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory

abstract:
  Changes are occurring within Brazilian institutes of higher education; currently several universities are reviewing their course offerings and teaching approaches to determine if they meet the needs of today's undergraduate students. When changes are made to the curriculum of experimental courses, there should be an understood guarantee that all efforts to avoid ethical and biosafety issues have been diligently considered. Ethical considerations lead us to create an alternative experimental session to be conducted that eliminated the use of rats, the conventional in vivo model employed for learning metabolism of glycogen in our university. To avoid possible biosafety issues, we prepared an alternative sample to simulate human urine, which we called guarurine. Using our new method, it is possible to verify positive results imitating a diabetic and starving people samples for detection of glucose and ketone. The alternative tool described herein is not only particularly suited to bypass the ethics of using animals for teaching, but also permits the discussion of significant aspects of pathological and physiological situations such as diabetics and starvation in a simple, safe, and interesting way.


id: cord-011485-15wtv6bt
title: An immunoassay cassette with a handheld reader for HIV urine testing in point-of-care diagnostics
author: Yang, Wenbo
date: 2020-05-21
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239691/
doi: 10.1007/s10544-020-00494-4
abstract:
  Currently, most HIV tests are performed with blood samples, or alternatively saliva samples are used for HIV testing. Simple HIV tests need to be performed in hospitals or other medical agencies instead of more invasive HIV blood tests. To enable point-of-care (POC) HIV diagnostics, based on a recently developed lateral flow strip for HIV urine testing, a microfluidic immunoassay cassette with a handheld optical reader is developed. Based on lateral flow strip with gold colloid reporter, the integrated immunoassay cassette can perform sample introduction, metering, discharging, applying and detection which simplifies HIV testing. An indicator is incorporated into the cassette to guide sample introduction based on color change, and further, the excess test sample is stored inside the sealed cassette to avoid any contamination. The low-cost handheld optical reader can provide a test result within a few seconds, which is useful for simple, sensitive and affordable HIV onsite detection. Instead of using normal white LEDs, a customized back light module embedded with green LEDs is adopted to illuminate the lateral flow strip with an appropriate working current to achieve optimal performance. Compared to the standard lateral flow strips using a benchtop reader, with the disposable immunoassay cassette assisted by the handheld optical reader, more convenient, easier-to-operate, and more affordable HIV urine testing can be achieved in POC diagnostics.


id: cord-015482-ovuofl9q
title: Probability Sampling by Connecting Space with Households Using GIS/GPS Technologies
author: Chen, Xinguang
date: 2018-01-23
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107540/
doi: 10.1093/jssam/smx032
abstract:
  Sampling methods for survey studies are challenged by the replacement of landline telephones with mobile phones, the lack of timely census data, and the growing need for studies to address new health challenges. GIS/GPS-assisted methods provide a promising alternative, but these methods need further improvement. We established a stratified 3-stage GIS/GPS-assisted sampling method in which residential areas of a target population are divided into mutually exclusive cells – geographic units (geounits) as the primary sampling frame (PSF). Geounits with residential households were randomly selected from the PSF with a semi-automatic algorithm implemented in R. Novel methods were used to sample households and participants. Simulations and application studies indicated adequate feasibility, efficiency and validity of the method in sampling rural-to-urban migrants from a large city with complex residential arrangements. With this method, researchers can determine sample size and number of geounits, households and participants to be sampled; optimally allocate geounits; determine area size of sampled geounits and estimate sample weights; and complete sampling for field data collection in a short period. Our method adds an integrative approach for GIS/GPS-assisted random sampling with a de facto population assumption. Additional evaluation studies are needed to assess the utility of this method in different settings.


id: cord-017248-a37t31u1
title: Alphabetic Listing of Diseases and Conditions
author: nan
date: 2010-05-17
txt: ./txt/cord-017248-a37t31u1.txt
cache: ./cache/cord-017248-a37t31u1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121759/
doi: 10.1007/978-1-59745-127-7_17
summary:
  Possible Associated Conditions: Disseminated intravascular coagulation;* eclampsia;* glucose-6-phosphatase deficiency (G6PD); hemolytic uremic syndrome;* malignant hypertension; lymphoma* and other malignancies; paroxysmal nocturnal hemo-globinuria; sickle cell disease;*thalassemia;* thrombotic thrombocytopenic purpura.* (See also below under "NOTE.") NOTE: Hemolysis also may be caused by conditions such as poisoning with chemicals or drugs, heat injury, snake bite,* or infections or may develop as a transfusion reaction* or be secondary to adenocarcinoma, heart valve prostheses (see below), liver disease (see below), renal disease, or congenital erythropoietic porphyria. Unusual under-lying or associated conditions include chronic aortic stenosis or regurgitation; coronary artery anomalies; coronary artery dissection; coronary embolism; coronary ostial stenosis (due to calcification of aortic sinotubular junction or, rarely, to syphilitic aortitis); coronary vasculitis (for instance, in polyarteritis nodosa* or acute hypersensitivity arteritis); hyperthyroidism,* gastrointestinal hemorrhage; * hypothyroidism, * idiopathic arterial calcification of infancy; intramural coronary amyloidosis; pheochromocytoma, polycythemia vera; * pseudoxanthoma elasticum,* radiationinduced coronary stenosis; severe pulmonary hypertension (with right ventricular ischemia); sickle cell disease;* and others.

abstract:
  Part II begins with a list of special histologic stains, their for use and their corresponding references. At the end of this list is a procedure for removal of formalin precipitate from tissue sections.


id: cord-017543-60q9iecq
title: Microfluidic Applications in Biodefense
author: Tian, Wei-Chang
date: 2008-08-23
txt: ./txt/cord-017543-60q9iecq.txt
cache: ./cache/cord-017543-60q9iecq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122129/
doi: 10.1007/978-0-387-09480-9_10
abstract: nan
summary:
  Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems.


id: cord-018761-vm86d4mj
title: Technical Annexes
author: Bradt, David A.
date: 2017-11-08
txt: ./txt/cord-018761-vm86d4mj.txt
cache: ./cache/cord-018761-vm86d4mj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123725/
doi: 10.1007/978-3-319-69871-7_8
abstract:
  This chapter provides guidance on technical issues in the health sector. The annexes contain selective compilations of frequently used reference information.


id: cord-022147-istz1iql
title: Procedures to Investigate Waterborne Illness
author: nan
date: 2016-07-13
txt: ./txt/cord-022147-istz1iql.txt
cache: ./cache/cord-022147-istz1iql.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153435/
doi: 10.1007/978-3-319-26027-3_1
summary:
  • Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers'' homes, are necessary to prevent further illness.

abstract:
  Humanity could not survive without a reliably clean, safe, and steady flow of drinking water. Since the early 1900s when typhoid fever and cholera were frequently causes of waterborne illness in developed countries, drinking water supplies have been protected and treated to ensure water safety, quality, and quantity. Having access to safe drinking water has always been one of the cornerstones of good public health. Not only safe water is limited to drinking water, but recreational water can also be a source for waterborne illness—both from treated waters such as in swimming pools, whirlpools, or splash pads and from non-treated surface waters such as lakes, rivers, streams and ponds. Recreational waters may cause illness not only from ingestion of pathogens, but also when in contact with eyes, ears, or skin. Some pathogens in water can be acquired by inhalation of aerosols from water that is agitated or sprayed such as in humidifiers, fountains, or misting of produce. This poses a potential risk to those exposed, particularly if they are immunocompromised.


id: cord-023095-4dannjjm
title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011
author: nan
date: 2011-05-03
txt: ./txt/cord-023095-4dannjjm.txt
cache: ./cache/cord-023095-4dannjjm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166756/
doi: 10.1111/j.1939-1676.2011.0726.x
abstract: nan
summary:
  The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] !


id: cord-023442-4vzwc2d2
title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA
author: nan
date: 2006-12-05
txt: ./txt/cord-023442-4vzwc2d2.txt
cache: ./cache/cord-023442-4vzwc2d2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169609/
doi: 10.1002/sca.4950160315
abstract: nan
summary:
  IV-4 Scanning Vol. 16, Supplement IV (1994) Simulation of image formation and detection systems in the SEM is a vital link in performing image analysis to obtain precise measurements, to provide the necessary connection between image parameters and structural dimensions, and to reflect important microscope beam and detector parameters. By knowing the transfer function, noise, and distortion figure in digital form, it is relatively easy to obtain more accurate comparison of the measured and calculated signal (Fig. 1 The calculation of image contrast in the scanning electron microscope (SEM) can be done using Monte Carlo techniques if the electron trajectories can be calculated through the composition profiles in the specimen. Specimens providing IV-18 Scanning Vol. 16, Supplement IV (1994) FIG highly redundant structures and relatively smooth fractures, such as cell suspensions or o/w emulsions, were investigated using freeze fracture/replication and ambient temperature transmission electron microscopy (AT-TEM).


id: cord-024503-f4ibgn9i
title: Self-supervised Learning for Semi-supervised Time Series Classification
author: Jawed, Shayan
date: 2020-04-17
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206263/
doi: 10.1007/978-3-030-47426-3_39
abstract:
  Self-supervised learning is a promising new technique for learning representative features in the absence of manual annotations. It is particularly efficient in cases where labeling the training data is expensive and tedious, naturally linking it to the semi-supervised learning paradigm. In this work, we propose a new semi-supervised time series classification model that leverages features learned from the self-supervised task on unlabeled data. The idea is to exploit the unlabeled training data with a forecasting task which provides a strong surrogate supervision signal for feature learning. We draw from established multi-task learning approaches and model forecasting as an auxiliary task to be optimized jointly with the main task of classification. We evaluate our proposed method on benchmark time series classification datasets in semi-supervised setting and are able to show that it significantly outperforms the state-of-the-art baselines.


id: cord-024553-jat7pttf
title: Correlation-Aware Deep Generative Model for Unsupervised Anomaly Detection
author: Fan, Haoyi
date: 2020-04-17
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206313/
doi: 10.1007/978-3-030-47436-2_52
abstract:
  Unsupervised anomaly detection aims to identify anomalous samples from highly complex and unstructured data, which is pervasive in both fundamental research and industrial applications. However, most existing methods neglect the complex correlation among data samples, which is important for capturing normal patterns from which the abnormal ones deviate. In this paper, we propose a method of Correlation aware unsupervised Anomaly detection via Deep Gaussian Mixture Model (CADGMM), which captures the complex correlation among data points for high-quality low-dimensional representation learning. More specifically, the relations among data samples are correlated firstly in forms of a graph structure, in which, the node denotes the sample and the edge denotes the correlation between two samples from the feature space. Then, a dual-encoder that consists of a graph encoder and a feature encoder, is employed to encode both the feature and correlation information of samples into the low-dimensional latent space jointly, followed by a decoder for data reconstruction. Finally, a separate estimation network as a Gaussian Mixture Model is utilized to estimate the density of the learned latent vector, and the anomalies can be detected by measuring the energy of the samples. Extensive experiments on real-world datasets demonstrate the effectiveness of the proposed method.


id: cord-030409-bwxkxvsl
title: Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate
author: Mamontov, Eugene
date: 2020-08-10
txt: ./txt/cord-030409-bwxkxvsl.txt
cache: ./cache/cord-030409-bwxkxvsl.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423024/
doi: 10.1021/acsomega.0c03091
summary:
  When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The free base HCQ and more ordered hydrated HCQS also show the methyl rotation peak at the same position, in agreement with their similar activation energies (for the broad dynamic component) presented in Figure 7 . This suggests that the effect of hydration on the activation energy for the methyl group rotation may be due to the disorder introduced by the water molecules in the main hydrated and less ordered hydrated HCQS samples. While the upper panels of Figures 10 and 11 show the measured spectra, the lower panels present a comparison of the difference spectra between the main hydrated and dry HCQS samples to the spectra of H 2 O ice-Ih (5 K) and liquid water (295 K) as well as the structural H 2 O in WO 3 ·H 2 O data.

abstract:
  [Image: see text] Chloroquine and its derivative hydroxychloroquine are primarily known as antimalaria drugs. Here, we investigate the influence of hydration water on the molecular dynamics in hydroxychloroquine sulfate, a commonly used solubilized drug form. When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The facilitated stochastic motions of the methyl groups may benefit the biomolecular activity due to the more efficient sampling of the energy landscape in the disordered hydration environment experienced by the drug molecules in vivo.


id: cord-030725-876arxiu
title: September 2020 New in Review
author: nan
date: 2020-08-20
txt: ./txt/cord-030725-876arxiu.txt
cache: ./cache/cord-030725-876arxiu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440878/
doi: 10.1016/j.jand.2020.07.010
abstract: nan
summary:
  Researchers assessed nutritional risks among older patients diagnosed with COVID-19 along with their associated clinical outcomes. The NRS 2002 was designed to predict clinical effects of nutritional treatment in hospital settings with two levels: level 1 and level 2 contained factors of BMI status, weight loss history, nutritional intake, and disease severity. Association of work requirements with Supplemental Nutrition Assistance Program participation by race/ ethnicity and disability status, 2013-2017. Dietary patterns studied included the Alternative Healthy Eating Index, Dietary Approaches to Stop Hypertension diet score, and Mediterranean-style, adherence to which was determined via the food frequency questionnaire. Association between lifestyle factors, vitamin and garlic supplementation, and gastric cancer outcomes: A secondary analysis of a randomized clinical trial. A secondary analysis of a randomized controlled trial was performed to examine this issue using a sample of 3,365 participants. Demographic variables taken included age, sex, race/ethnicity, participation in the Supplemental Nutrition Assistance Program, family income level, education of parents, and health insurance status.


id: cord-031907-ilhr3iu5
title: ISEV2020 Abstract Book
author: nan
date: 2020-07-15
txt: ./txt/cord-031907-ilhr3iu5.txt
cache: ./cache/cord-031907-ilhr3iu5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/
doi: 10.1080/20013078.2020.1784511
abstract: nan
summary:
  L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma.


id: cord-102471-dtukacm7
author: Xu, Y.
date: 2020-04-22
url: http://medrxiv.org/cgi/content/short/2020.04.21.20073072v1?rss=1
doi: 10.1101/2020.04.21.20073072
title:
  Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission

abstract:
  Background: Influenza virus presents a significant challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid diagnosis of infection, rationalising antimicrobial therapy, and supporting interventions for infection control. This study aimed to evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings. Methods: We conducted Nanopore metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic testing. We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data. Results: Metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses compared with the diagnostic standard (Cepheid Xpress/BioFire FilmArray Respiratory Panel). We identified a H3N2 genome with the oseltamivir resistant S331R mutation in the NA protein, potentially associated with the emergence of a distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in the infectious diseases ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant strain circulating in the community. We also detected a range of other potentially pathogenic viruses and bacteria from the metagenome. Conclusion: Nanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Generation of full genomes can contribute to the investigation and management of nosocomial outbreaks.


id: cord-102547-nxut8ov1
author: GraÌdel, C.
date: 2020-06-09
txt: ./txt/cord-102547-nxut8ov1.txt
cache: ./cache/cord-102547-nxut8ov1.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.06.09.20126219v1?rss=1
doi: 10.1101/2020.06.09.20126219
summary:
  DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. Taxonomic classification of viral reads (Oxford Nanopore) and contigs (Illumina MiSeq) using MEGAN based on BLASTN matches against NCBI''s nucleotide (nt) database at the species and genotype levels. In order to confirm the genotype identification and to obtain a highly accurate whole genome sequence of the enterovirus genome, we subsequently subjected the sample E590 also to cDNA sequencing using Illumina MiSeq. In this case, the cDNA was produced using genotype-specific primers given that low number of reads was obtained by DRS and MiSeq . Illumina sequencing of the cDNA from sample E026 produced using oligo-dT primers and random hexamers showed similar distributions on the domain level: The majority of contigs belonged to bacterial species (98.6% and 98.9%, respectively for oligo-dT and random hexamer approaches), with a minority of reads mapping to eukaryotes (0.49%, 0.50%) and viruses (0.87%, 0.56%).

title:
  Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing

abstract:
  Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load.


id: cord-102613-hly07ne3
title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
author: Danko, David
date: 2020-05-04
txt: ./txt/cord-102613-hly07ne3.txt
cache: ./cache/cord-102613-hly07ne3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/724526
doi: 10.1101/724526
summary:
  We identified covariates which influenced the taxonomic composition 204 of our samples: city, population density, average temperature in June, region, elevation above sea-level, 205 surface type, surface material, elevation above or below ground and proximity to the coast. To quantify how the principle covariates, climate, continent, and surface material impacted the taxo-213 nomic composition of samples, we performed a Principal Component Analysis (PCA) on our taxonomic 214 data normalized by proportion and identified principal components (PCs) which were strongly associated 215 with a metadata covariate in a positive or negative direction (PCs were centered so an average direction 216 indicates an association). In general, negative controls had 798 lower k-mer complexity, fewer reads, and lower post PCR Qubit scores than case samples and no major Previous studies have reported that microbial species whose relative abundance is negatively cor-803 related with DNA concentration may be contaminants.

abstract:
  Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, there are no systematic worldwide studies of these dense, human microbial ecosystems. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 60 cities, spanning 4,728 samples and 4,424 taxonomically-defined microorganisms collected for three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance markers, and novel genetic elements, including 10,928 novel predicted viral species, 1302 novel bacteria, and 2 novel archaea. Urban microbiomes often resemble human commensal microbiomes from the skin and airways, but also contain a consistent “core” of 31 species which are predominantly not human commensal species. Samples show distinct microbial signatures which may be used to accurately predict properties of their city of origin including population, proximity to the coast, and taxonomic profile. These data also show that AMR density across cities varies by several orders of magnitude, including many AMRs present on plasmids with cosmopolitan distributions. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s cities.


id: cord-103180-5hkoeca7
title: Sample pooling methods for efficient pathogen screening: Practical implications
author: Furstenau, Tara N.
date: 2020-07-16
url: https://doi.org/10.1101/2020.07.16.206060
doi: 10.1101/2020.07.16.206060
abstract:
  Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.


id: cord-103735-nil1vv6h
title: Non-invasive surveys of mammalian viruses using environmental DNA
author: Alfano, Niccolo
date: 2020-03-29
txt: ./txt/cord-103735-nil1vv6h.txt
cache: ./cache/cord-103735-nil1vv6h.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.03.26.009993
doi: 10.1101/2020.03.26.009993
summary:
  Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses.

abstract:
  Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence.


id: cord-130198-pyg81vwb
title: Temporal Mental Health Dynamics on Social Media
author: Tabak, Tom
date: 2020-08-30
url: https://arxiv.org/pdf/2008.13121v3.pdf
doi: nan
abstract:
  We describe a set of experiments for building a temporal mental health dynamics system. We utilise a pre-existing methodology for distant-supervision of mental health data mining from social media platforms and deploy the system during the global COVID-19 pandemic as a case study. Despite the challenging nature of the task, we produce encouraging results, both explicit to the global pandemic and implicit to a global phenomenon, Christmas Depression, supported by the literature. We propose a methodology for providing insight into temporal mental health dynamics to be utilised for strategic decision-making.


id: cord-254596-wsmnlnlk
author: Grädel, Carole
date: 2020-07-31
url: https://doi.org/10.3390/v12080841
doi: 10.3390/v12080841
title:
  Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing

abstract:
  Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.


id: cord-254963-cnvxlv6h
author: Paskey, Adrian C.
date: 2019-02-26
url: https://doi.org/10.1186/s12864-019-5543-2
doi: 10.1186/s12864-019-5543-2
title:
  Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

abstract:
  BACKGROUND: Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS: Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users.


id: cord-258014-lzzi4rnz
author: Chorna, Nataliya
date: 2020-04-08
url: https://doi.org/10.3390/biomedicines8040081
doi: 10.3390/biomedicines8040081
title:
  A Protocol for the Multi-Omic Integration of Cervical Microbiota and Urine Metabolomics to Understand Human Papillomavirus (HPV)-Driven Dysbiosis

abstract:
  The multi-omic integration of microbiota data with metabolomics has gained popularity. This protocol is based on a human multi-omics study, integrating cervicovaginal microbiota, HPV status and neoplasia, with urinary metabolites. Indeed, to understand the biology of the infections and to develop adequate interventions for cervical cancer prevention, studies are needed to characterize in detail the cervical microbiota and understand the systemic metabolome. This article is a detailed protocol for the multi-omic integration of cervical microbiota and urine metabolome to shed light on the systemic effects of cervical dysbioses associated with Human Papillomavirus (HPV) infections. This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches.


id: cord-263831-7aj9ozpn
title: Increasing Virus Test Capacity via Recursive Pool Testing with an Application to SARS-CoV-2 Testing
author: Mutzel, P.
date: 2020-07-04
url: https://doi.org/10.1101/2020.07.02.20144956
doi: 10.1101/2020.07.02.20144956
abstract:
  In the context of adequate reactions to the current Covid-19 pandemic, Seifried, Ciesek et al. [6, 5] have proposed the application of SARS-CoV-2 pool testing in the pursuit of increasing testing capacity. We show how this method can be substantially improved in realistic scenarios, and we point out a possible impact on the ongoing discussion concerning the need of increased testing as a complementary measure to relaxed restrictions.


id: cord-273495-hruq0hdw
title: Composition analysis of falsified chloroquine phosphate samples seized during the COVID-19 pandemic
author: Waffo Tchounga, C.A.
date: 2020-11-12
url: https://www.sciencedirect.com/science/article/pii/S0731708520316472?v=s5
doi: 10.1016/j.jpba.2020.113761
abstract:
  The proliferation of falsified medicines can cause serious public health issues, particularly in the context of a global pandemic such as the actual COVID-19 pandemic. Our study involved eight chloroquine phosphate medicines seized in Cameroon, Democratic Republic of Congo and Niger during March and May 2020. These suspect samples were first analyzed in a screening phase using field tools such as handheld Raman spectroscopy (TruScan) and then in a confirmation phase using laboratory tools such as hyperspectral Raman imaging and High Performance Liquid Chromatography (HPLC). The results confirmed the falsified nature of the samples, highlighting the presence of metronidazole at low dose in four samples (16.6, 15.2, 15.2 and 14.5 mg/tab), too low levels of chloroquine in two samples (2.4 and 20.2 mg/tab), and substitution of chloroquine phosphate by paracetamol in one sample (255.7 mg/tab). The results also confirmed that four samples had been adulterated with paracetamol in trace amounts and two of them presented traces of chloramphenicol.


id: cord-275360-uphdzj5l
title: Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19)
author: Sahajpal, Nikhil Shri
date: 2020-07-30
url: https://www.sciencedirect.com/science/article/pii/S1525157820304074?v=s5
doi: 10.1016/j.jmoldx.2020.07.001
abstract:
  Testing for SARS-CoV-2 has lagged behind in many countries due to lack of adequate test kits and bottlenecks in the analytical process. The aim of this study was to investigate the feasibility and accuracy of a sample pooling approach for wide-scale population screening for COVID-19. A total of 940 nasopharyngeal-swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were de-identified and assigned random numbers for analysis. From this, 94 pools of 10 samples each were created. Automated RNA extraction followed by RT-PCR was carried out in a 96 well plate. Positive pools were identified and the individual samples were re-analyzed.


id: cord-280846-bbv6f5gf
title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America
author: Greninger, Alexander L.
date: 2010-10-18
url: https://doi.org/10.1371/journal.pone.0013381
doi: 10.1371/journal.pone.0013381
abstract:
  Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings.


id: cord-281916-v6u5mr2i
author: Bonnin, Paul
date: 2016-08-09
txt: ./txt/cord-281916-v6u5mr2i.txt
cache: ./cache/cord-281916-v6u5mr2i.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12879-016-1730-9
doi: 10.1186/s12879-016-1730-9
summary:
  METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. If a rich cell collection appears to be an important prerequisite for the quality of respiratory viral diagnosis, there is currently no information on a possible cellularity threshold that would validate the result of the viral molecular detection. These 800 aliquots were selected in the laboratory samples bank according to their results in virological diagnosis: 400 Positive and 400 Negative for molecular detection of respiratory panel using the RespiFinder ® Smart_22_Fast technique (Pathofinder, Maastricht, Netherlands). The main objectives of this work have been to study the cellularity of these clinical respiratory specimens, to propose a possible definition of what is commonly called "cellular richness," and to measure the impact of this marker on the molecular viral diagnosis. (2014) performed a molecular cell quantification using real time PCR in order to validate viral detection on nasal swabs.

title:
  Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice

abstract:
  BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale.


id: cord-288202-r3r2bc7v
author: Morel, Noelia
date: 2013-01-10
url: https://www.ncbi.nlm.nih.gov/pubmed/23326610/
doi: 10.1371/journal.pntd.0001967
title:
  A Monoclonal Antibody-Based Copro-ELISA Kit for Canine Echinococcosis to Support the PAHO Effort for Hydatid Disease Control in South America

abstract:
  Cystic echinococcosis is still a major concern in South America. While some regions show advances in the control of the disease, others have among the highest incidence in the world. To reverse this situation the Pan American Health Organization (PAHO) has launched a regional project on cystic echinococcosis control and surveillance. An early concern of the program was the lack of a standardized diagnostic tool to monitor infection in dogs, a key target of control programs. Under this premise, we have developed a new copro-ELISA test after extensive screening of a large panel of monoclonal antibodies (MAbs) and polyclonal sera, which performs with high standards of sensitivity (92.6%) and specificity (86.4%) as established by necropsy diagnosis of dogs. The key component of the test, MAbEg9 has a convenient IgG isotype and reacts with a periodate-resistant epitope found in high molecular weight components of the worm. Time-course analysis of experimentally infected dogs showed that even animals with a very low number of parasites could be detected as early as day 20 post infection. The test was formulated in a ready-to-use kit format with proven stability of each component for a minimum of 3 months at room temperature. This characteristic facilitates its standardized use and shipping to other laboratories, which was demonstrated by the identical results obtained by two different laboratories in Peru and our own laboratory when a large number of field samples were analyzed independently in a blind fashion.


id: cord-290722-neqj85xf
title: Faecal virome of red foxes from peri-urban areas
author: Lojkić, Ivana
date: 2016-01-29
url: https://www.sciencedirect.com/science/article/pii/S0147957116300121
doi: 10.1016/j.cimid.2016.01.005
abstract:
  Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N = 1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses.


id: cord-294062-3esrg1jw
author: Tam, Clarence C.
date: 2018-09-14
url: https://doi.org/10.1186/s12879-018-3358-4
doi: 10.1186/s12879-018-3358-4
title:
  Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study

abstract:
  BACKGROUND: Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS: We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS: We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS: Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3358-4) contains supplementary material, which is available to authorized users.


id: cord-298295-epxd03pt
author: Eckermann, M.
date: 2020-06-23
txt: ./txt/cord-298295-epxd03pt.txt
cache: ./cache/cord-298295-epxd03pt.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.06.21.20134882v1?rss=1
doi: 10.1101/2020.06.21.20134882
summary:
  We present a new approach of three-dimensional (3d) virtual histology and patho-histology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal-architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we can propose multi-scale phase contrast x-ray tomography as a novel tool to unravel the patho-physiology of Covid-19, extending conventional histology by a third dimension and allowing for a full quantification of tissue remodeling.By combining parallel and cone beam geometry, autopsy samples with a cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. The 3d virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated xray optics and instrumentation to image the tissue structure on multiple length scales, while at the same time covering large reconstruction volumes.

title:
  3d Virtual Patho-Histology of Lung Tissue from Covid-19 Patients based on Phase Contrast X-ray Tomography

abstract:
  We present a new approach of three-dimensional (3d) virtual histology and patho-histology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal-architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we can propose multi-scale phase contrast x-ray tomography as a novel tool to unravel the patho-physiology of Covid-19, extending conventional histology by a third dimension and allowing for a full quantification of tissue remodeling.By combining parallel and cone beam geometry, autopsy samples with a cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 160nm. We exemplify the capability of this approach by 3d visualisation of the diffuse alveolar damage with its prominent hyaline membrane formation, by mapping the 3d distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.


id: cord-298697-v1qdizwx
title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION
author: Chang, Jia Jin Marc
date: 2020-09-24
url: https://www.ncbi.nlm.nih.gov/pubmed/32987804/
doi: 10.3390/genes11101121
abstract:
  Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.


id: cord-300399-21xozruq
author: Jayamohan, Harikrishnan
date: 2020-10-18
url: https://www.ncbi.nlm.nih.gov/pubmed/33073312/
doi: 10.1007/s00216-020-02958-1
title:
  SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

abstract:
  The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification–, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.


id: cord-301823-fbeb1nw1
author: Sridhar, Sushmita
date: 2020-10-21
txt: ./txt/cord-301823-fbeb1nw1.txt
cache: ./cache/cord-301823-fbeb1nw1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33134554/
doi: 10.12688/wellcomeopenres.15937.2
summary:
  Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe.

title:
  A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities

abstract:
  The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame.


id: cord-301991-n87le8ix
title: Diatoms recovery from wastewater: Overview from an ecological and economic perspective
author: Saxena, Abhishek
date: 2020-10-16
txt: ./txt/cord-301991-n87le8ix.txt
cache: ./cache/cord-301991-n87le8ix.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S2214714420305833
doi: 10.1016/j.jwpe.2020.101705
summary:
  Because diatoms produce organic matter to a large extent that permits natural inbuilt capacity to withstand toxicity levels in water bodies, extended survival rate, short regeneration time than microalgae, fishes, and other micro invertebrates thus making them one of the best candidate for water quality monitoring, and excellent bioindicators of aquatic biological integrity [12, 13] . Isolation and identification of benthic diatoms are problematic in comparison with planktonic species due to difficulties in sample treatment, sampling, and microscopic observation though benthic diatoms play the main role as bioindicators in the aquatic ecosystem because they attached to the substratum with secreted mucilage from their cell wall [44, 45] . An outline of isolation of pure diatom species getting affected by the surrounding contaminants is challenging since they get heavily occupied with different interfering organisms, which pose a significant threat in obtaining axenic culture, as presented in Fig. 3 .

abstract:
  Alarming water pollution is toxic to the aquatic ecosystem leading to a sharp decline in species diversity. Diatoms have great potency to survive in contaminated water bodies, hence they can be compelling bioindicators to monitor the change in the environmental matrices effectively. Around the globe, researchers are intended to evaluate the impact of pollution on the diatoms recovery and techniques used for the assessment. The diatoms are precious for futuristic need viz. value-added products, energy generation, pharmaceuticals, and aquaculture feedstocks. All these applications led to a significant rise in diatoms research among the scientific community. This review presents different isolation practices, cultivation, and other challenges associated with the diatoms. A precise focus is given to diatoms isolation techniques from highly polluted water bodies with the main thrust towards obtaining an axenic culture to elucidate the significance of pure diatom cultures. Recovery of “jewels of the sea” from polluted water signifies the prospective ecological and economic aspects.


id: cord-303647-c4umbcvn
title: A New Approach for Monitoring Ebolavirus in Wild Great Apes
author: Reed, Patricia E.
date: 2014-09-18
url: https://www.ncbi.nlm.nih.gov/pubmed/25232832/
doi: 10.1371/journal.pntd.0003143
abstract:
  BACKGROUND: Central Africa is a “hotspot” for emerging infectious diseases (EIDs) of global and local importance, and a current outbreak of ebolavirus is affecting multiple countries simultaneously. Ebolavirus is suspected to have caused recent declines in resident great apes. While ebolavirus vaccines have been proposed as an intervention to protect apes, their effectiveness would be improved if we could diagnostically confirm Ebola virus disease (EVD) as the cause of die-offs, establish ebolavirus geographical distribution, identify immunologically naïve populations, and determine whether apes survive virus exposure. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first successful noninvasive detection of antibodies against Ebola virus (EBOV) from wild ape feces. Using this method, we have been able to identify gorillas with antibodies to EBOV with an overall prevalence rate reaching 10% on average, demonstrating that EBOV exposure or infection is not uniformly lethal in this species. Furthermore, evidence of antibodies was identified in gorillas thought previously to be unexposed to EBOV (protected from exposure by rivers as topological barriers of transmission). CONCLUSIONS/SIGNIFICANCE: Our new approach will contribute to a strategy to protect apes from future EBOV infections by early detection of increased incidence of exposure, by identifying immunologically naïve at-risk populations as potential targets for vaccination, and by providing a means to track vaccine efficacy if such intervention is deemed appropriate. Finally, since human EVD is linked to contact with infected wildlife carcasses, efforts aimed at identifying great ape outbreaks could have a profound impact on public health in local communities, where EBOV causes case-fatality rates of up to 88%.


id: cord-305282-x2zzzw43
title: Feasibility of Reusing Surgical Mask Under Different Disinfection Treatments
author: SUEN, C. Y.
date: 2020-05-20
url: http://medrxiv.org/cgi/content/short/2020.05.16.20102178v1?rss=1
doi: 10.1101/2020.05.16.20102178
abstract:
  The possibility to extend the lifespan or even reuse one-off personal protective equipment, especially for N95 respirator and surgical mask become critical during pandemic. World Health Organization has confirmed that wearing surgical mask is effective in controlling the spread of respiratory diseases in the community, but the supply may not be able to satisfy all the demands created all over the world in a short period of time. This investigation found that dry heat and UVC irradiance could effectively disinfect the mask material without creating significant damage to surgical mask.


id: cord-305755-6jup93v4
author: Gouveia, Duarte
date: 2020-07-22
url: https://www.ncbi.nlm.nih.gov/pubmed/32697082/
doi: 10.1021/acs.jproteome.0c00535
title:
  Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

abstract:
  [Image: see text] Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.


id: cord-307261-0a3iztns
author: Hayden, Randall T.
date: 2012-01-30
url: https://www.sciencedirect.com/science/article/pii/S1386653211005531
doi: 10.1016/j.jcv.2011.12.020
title:
  Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children

abstract:
  BACKGROUND: The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens. OBJECTIVES: Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children. STUDY DESIGN: A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected. RESULTS: The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen. CONCLUSIONS: Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens.


id: cord-307874-0obomty2
title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis?
author: Pardon, Bart
date: 2020-05-23
txt: ./txt/cord-307874-0obomty2.txt
cache: ./cache/cord-307874-0obomty2.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0749072020300220
doi: 10.1016/j.cvfa.2020.03.005
summary:
  Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity.

abstract:
  When it is desired to identify infectious agents involved in an outbreak of bovine respiratory disease, a variety of possible sampling methods may be used. For field use, the deep nasopharyngeal swab, transtracheal wash, and nonendoscopic bronchoalveolar lavage are most feasible. At present, bacterial culture and polymerase chain reaction testing are most commonly used to identify infectious agents. Interpretation of test results can be challenging, particularly for opportunistic pathogens. Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented.


id: cord-308687-wrzzb9cy
title: Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals
author: Brunner, Jesse L.
date: 2020-06-24
txt: ./txt/cord-308687-wrzzb9cy.txt
cache: ./cache/cord-308687-wrzzb9cy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32581260/
doi: 10.1038/s41598-020-66280-7
summary:
  swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. www.nature.com/scientificreports www.nature.com/scientificreports/ context of screening U.S. service members for syphilis, pooling samples to reduce the number of tests required to detect rare infections is common in numerous contexts 22 , including surveys for disease freedom. In this paper I therefore develop formulae for imperfect tests of pooled samples in closed populations and eDNA, discuss the key assumptions and considerations in their application, and illustrate how eDNA may be especially useful for detecting infections in the live animal trade. Pooling and batch-processing samples collected from individual animals (e.g., swabs) can reduce several fold the number of diagnostic tests (e.g., DNA extractions and PCR reactions) required to detect rare infections.

abstract:
  The regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved—hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DNA (eDNA)—the genetic material shed into an organism’s environment—collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDNA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts.


id: cord-310061-nro623aa
title: Detection of novel coronaviruses in bats in Myanmar
author: Valitutto, Marc T.
date: 2020-04-09
url: https://www.ncbi.nlm.nih.gov/pubmed/32271768/
doi: 10.1371/journal.pone.0230802
abstract:
  The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.


id: cord-313107-6cfenpxm
author: Singh, Anirudh K.
date: 2020-09-22
txt: ./txt/cord-313107-6cfenpxm.txt
cache: ./cache/cord-313107-6cfenpxm.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32960929/
doi: 10.1371/journal.pone.0239492
summary:
  In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs.

title:
  Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study

abstract:
  Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated.


id: cord-313670-tbah33ro
title: Regulation of Biobanks in Italy
author: Cannovo, Nunzia
date: 2020-09-02
txt: ./txt/cord-313670-tbah33ro.txt
cache: ./cache/cord-313670-tbah33ro.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32984196/
doi: 10.3389/fped.2020.00415
summary:
  In Italy, a biobank is "a non-profit organization that must be officially recognized by the appropriate healthcare authority in the member states and must guarantee the treatment, distribution and conservation of biological material according to standards of quality and professionalism," but must not conserve material already regulated by specific laws, as is the case for organs for transplants, blood for transfusions, as well as embryos and gametes for medically assisted reproduction. It can be said that a biobank is "a structured collection of human biological material accessible on the basis of certain criteria" (3, 4) , "in accordance with a code of good practice and correct behavior and with further indications provided by ethics committees and universities" (5) and "in which the information contained in the biological material can be traced to a specific person" (2), "for diagnostic, treatment and research purposes" (6) .

abstract:
  In Italy, a biobank is “a non-profit organization that must be officially recognized by the appropriate healthcare authority in the member states and must guarantee the treatment, distribution and conservation of biological material according to standards of quality and professionalism,” but must not conserve material already regulated by specific laws, as is the case for organs for transplants, blood for transfusions, as well as embryos and gametes for medically assisted reproduction. The concept of biobank includes not only biological samples, but also the related database of clinical and personal information, from which the subject's lifestyle can be deduced. Unfortunately, at the moment, Italian law does not offer specific itineraries for achieving this legal status.


id: cord-313887-8sabsrgy
author: Quandt, Sara A.
date: 2020-08-10
txt: ./txt/cord-313887-8sabsrgy.txt
cache: ./cache/cord-313887-8sabsrgy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32785108/
doi: 10.3390/ijerph17165786
summary:
  Taken together, the rapidly changing messages, coupled with public concern, and limited availability of up-to-date information in formats for those with limited English proficiency created a situation in the USA in which Latinx workers such as farmworkers were likely to lack consistent and accurate information and, as a result, practice ineffective behaviors to protect themselves and prevent spreading disease to their social network. This study was designed to describe the knowledge, perceived risk and susceptibility, and preventive behaviors reported by Latinx immigrant farmworker and nonfarmworker families in North Carolina during the first months of the COVID-19 pandemic. In total, these results indicate that, despite relatively high knowledge, strong perceptions of risk from COVID-19, and claims of avoiding situations where contracting or spreading infection might be likely, many of the farmworker families included here do not practice safe physical distancing measures as recommended; and their use of masks appears to be confined to work settings.

title:
  COVID-19 Pandemic among Latinx Farmworker and Nonfarmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors

abstract:
  (1) Background: The COVID-19 pandemic poses substantial threats to Latinx farmworkers and other immigrants in food production and processing. Classified as essential, such workers cannot shelter at home. Therefore, knowledge and preventive behaviors are important to reduce COVID-19 spread in the community. (2) Methods: Respondents for 67 families with at least one farmworker (FWF) and 38 comparable families with no farmworkers (nonFWF) in North Carolina completed a telephone survey in May 2020. The survey queried knowledge of COVID-19, perceptions of its severity, self-efficacy, and preventive behaviors. Detailed data were collected to document household members’ social interaction and use of face coverings. (3) Results: Knowledge of COVID-19 and prevention methods was high in both groups, as was its perceived severity. NonFWF had higher self-efficacy for preventing infection. Both groups claimed to practice preventive behaviors, though FWF emphasized social avoidance and nonFWF emphasized personal hygiene. Detailed social interactions showed high rates of inter-personal contact at home, at work, and in the community with more mask use in nonFWF than FWF. (4) Conclusions: Despite high levels of knowledge and perceived severity for COVID-19, these immigrant families were engaged in frequent interpersonal contact that could expose community members and themselves to COVID-19.


id: cord-314503-u1y1bznk
title: A perspective on microarrays: current applications, pitfalls, and potential uses
author: Jaluria, Pratik
date: 2007-01-25
txt: ./txt/cord-314503-u1y1bznk.txt
cache: ./cache/cord-314503-u1y1bznk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17254338/
doi: 10.1186/1475-2859-6-4
summary:
  Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Several organizations such as the Microarray Gene Expression Data (MGED) Society and the European Bioinformatics Institute (EBI) have established guidelines to aid researchers in the design and implementation of microarray experiments [8, 9, 16] . As mentioned earlier, verification is critical in order to assign distinct expression patterns to specific genes with certainty (i.e. statistical significance) because of the inherent variability present in microarray data. To verify the results generated from microarray experiments, a combinatorial approach is usually needed; checking the statistical significance associated with the expression levels of specific genes, reviewing the literature, and conducting additional experiments such as RT-PCR or Northern blotting. A large number of microarray-related studies in the past have aimed to either characterize diseased cells in comparison to healthy cells or highlight the genes involved in a particular biological pathway [4, 8] .

abstract:
  With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold.


id: cord-314753-xflhxb13
title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
author: Manso, Carmen F.
date: 2017-06-23
txt: ./txt/cord-314753-xflhxb13.txt
cache: ./cache/cord-314753-xflhxb13.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28646219/
doi: 10.1038/s41598-017-02239-5
summary:
  The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration.

abstract:
  RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 10(4) and 10(3) IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.


id: cord-315054-kji2kfek
author: Chakraborty, Nabarun
date: 2020-07-22
url: https://doi.org/10.3389/fmolb.2020.00142
doi: 10.3389/fmolb.2020.00142
title:
  Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration

abstract:
  At the heart of the phenome-to-genome approach is high throughput assays, which are liable to produce false results. This risk can be mitigated by minimizing the sample bias, specifically, recycling the same tissue specimen for both phenotypic and genotypic investigations. Therefore, our aim is to suggest a methodology of obtaining robust results from frozen specimens of compromised quality, particularly if the sample is produced in conditions with limited resources. For example, generating samples at the International Space Station (ISS) is challenging because the time and laboratory footprint allotted to a project can get expensive. In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. We further optimized a method to sequester the tissue specimen from the H&E slides using an incubator shaker. Using this method, we were able to recover an optimal amount of RNA that could be used for downstream transcriptomics assays. Overall, we demonstrated a protocol that enables us to maximize scientific values from tissues collected in austere condition. Furthermore, our protocol can suggest an improvement in the spatial resolution of transcriptomic assays.


id: cord-317213-vhprfb1o
author: Tram, Dai Thien Nhan
date: 2016-09-26
url: https://www.ncbi.nlm.nih.gov/pubmed/27686397/
doi: 10.1016/j.biotechadv.2016.09.003
title:
  Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases

abstract:
  Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases.


id: cord-319685-dw0qsl4s
author: Porter, Emily
date: 2014-04-25
url: https://www.ncbi.nlm.nih.gov/pubmed/24767677/
doi: 10.1186/1297-9716-45-49
title:
  Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis

abstract:
  Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. In cats with FIP, 95% of tissue, and 81% of faecal samples were PCR-positive, as opposed to 22% of tissue, and 60% of faecal samples in cats without FIP. Relative FCoV copy numbers were significantly higher in the cats with FIP, both in tissues (P < 0.001) and faeces (P = 0.02). PCR-positive samples underwent pyrosequencing encompassing position 1058 of the FCoV spike protein. This identified a methionine codon at position 1058, consistent with the shedding of an enteric form of FCoV, in 77% of the faecal samples from cats with FIP, and in 100% of the samples from cats without FIP. In contrast, 91% of the tissue samples from cats with FIP and 89% from cats without FIP had a leucine codon at position 1058, consistent with a systemic form of FCoV. These results suggest that the methionine to leucine substitution at position 1058 in the FCoV spike protein is indicative of systemic spread of FCoV from the intestine, rather than a virus with the potential to cause FIP.


id: cord-321549-r7bmtloy
title: Scent dog identification of samples from COVID-19 patients – a pilot study
author: Jendrny, Paula
date: 2020-07-23
url: https://www.ncbi.nlm.nih.gov/pubmed/32703188/
doi: 10.1186/s12879-020-05281-3
abstract:
  BACKGROUND: As the COVID-19 pandemic continues to spread, early, ideally real-time, identification of SARS-CoV-2 infected individuals is pivotal in interrupting infection chains. Volatile organic compounds produced during respiratory infections can cause specific scent imprints, which can be detected by trained dogs with a high rate of precision. METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. RESULTS: The dogs were able to discriminate between samples of infected (positive) and non-infected (negative) individuals with average diagnostic sensitivity of 82.63% (95% confidence interval [CI]: 82.02–83.24%) and specificity of 96.35% (95% CI: 96.31–96.39%). During the presentation of 1012 randomised samples, the dogs achieved an overall average detection rate of 94% (±3.4%) with 157 correct indications of positive, 792 correct rejections of negative, 33 incorrect indications of negative or incorrect rejections of 30 positive sample presentations. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. This data may form the basis for the reliable screening method of SARS-CoV-2 infected people.


id: cord-323973-wszo9s3d
title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond
author: Zhu, Hanliang
date: 2020-07-20
txt: ./txt/cord-323973-wszo9s3d.txt
cache: ./cache/cord-323973-wszo9s3d.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0165993620302132
doi: 10.1016/j.trac.2020.115984
summary:
  [9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa.

abstract:
  Infectious diseases, such as the most recent case of COVID-19, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfilling this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.


id: cord-324944-ixh3ykrc
title: Diagnostic tools for tackling febrile illness and enhancing patient management
author: Mitsakakis, Konstantinos
date: 2018-12-05
txt: ./txt/cord-324944-ixh3ykrc.txt
cache: ./cache/cord-324944-ixh3ykrc.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0167931718304556
doi: 10.1016/j.mee.2018.10.001
summary:
  This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases).

abstract:
  Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem.


id: cord-326133-d46wbfrx
author: Nakayasu, Ernesto S.
date: 2016-05-10
txt: ./txt/cord-326133-d46wbfrx.txt
cache: ./cache/cord-326133-d46wbfrx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27822525/
doi: 10.1128/msystems.00043-16
summary:
  We then applied this methodology and integrated proteomic, lipidomic, and metabolomic analyses in the study of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in a lung epithelial cell line, which showed the impact of viral infection on different host metabolic pathways. We then evaluated if these protein losses affected the ability to obtain useful proteomic data, since a method that can simultaneously extract multiple omics sources from the same sample would be extremely useful for systems biology experiments and subsequent integrated data analysis, as well as in cases where limited sample amounts are available (e.g., a survey of data from the National Cancer Institute showed that obtaining an adequate number of samples to conduct a study is a major difficulty facing researchers [21] ).

title:
  MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

abstract:
  Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available.


id: cord-326380-9ecsp66y
title: Assessment of sample pooling for clinical SARS-CoV-2 testing
author: Griesemer, Sara B
date: 2020-05-27
url: https://doi.org/10.1101/2020.05.26.118133
doi: 10.1101/2020.05.26.118133
abstract:
  Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as barcoding, electronic data transfer and extensive robotics, throughput capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to further address this need. The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples across ten weeks of the pandemic were reviewed. Weak positive specimens were detected in all five-sample pools but failed to be detected in four of the 24 nine-sample pools tested. Weak positive samples comprised an average 16.5% of the positive specimens tested during the pandemic thus far, slightly increasing in frequency during later weeks. Other aspects of the testing process should be considered, however, such as accessioning and reporting, which are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.


id: cord-329162-6w8qcv1c
author: Ayginin, Andrey A.
date: 2018-08-12
txt: ./txt/cord-329162-6w8qcv1c.txt
cache: ./cache/cord-329162-6w8qcv1c.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2018/3248285
doi: 10.1155/2018/3248285
summary:
  The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format.

title:
  The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

abstract:
  Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.


id: cord-333413-8buawes0
author: Liebing, J.
date: 2020-06-16
txt: ./txt/cord-333413-8buawes0.txt
cache: ./cache/cord-333413-8buawes0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32544211/
doi: 10.1371/journal.pone.0234044
summary:
  Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations.

title:
  Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany

abstract:
  Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. Contributing factors to the ongoing negative trend, such as the effects of pesticides, diseases, predation, increase in traffic and reduced fallow periods, are currently being controversially discussed. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. The pheasant chicks were divided into three age groups to detect differences in their development and physical constitution. In addition, pathomorphological, parasitological, virological, bacteriological and toxicological investigations were performed. The younger chicks were emaciated, while the older chicks were of moderate to good nutritional status. However, the latter age group was limited to a maximum of three chicks per hen, while the youngest age class comprised up to ten chicks. The majority of chicks suffered from dermatitis of the periocular and caudal region of the head (57–94%) of unknown origin. In addition, intestinal enteritis (100%), pneumonia (26%), hepatitis (24%), perineuritis (6%), tracheitis (24%), muscle degeneration (1%) and myositis (1%) were found. In 78% of the cases, various Mycoplasma spp. were isolated. Mycoplasma gallisepticum (MG) was not detected using an MG-specific PCR. Parasitic infections included Philopteridae (55%), Coccidia (48%), Heterakis/Ascaridia spp. (8%) and Syngamus trachea (13%). A total of 8% of the chicks were Avian metapneumovirus (AMPV) positive using RT-PCR, 16% positive for infectious bronchitis virus (IBV) using RT-PCR, and 2% positive for haemorrhagic enteritis virus (HEV) using PCR. All samples tested for avian encephalomyelitis virus (AEV), infectious bursal disease virus (IBDV) or infectious laryngotracheitis virus (ILTV) were negative. The pool samples of the ten chicks were negative for all acid, alkaline-free and derivative substances, while two out of three samples tested were positive for the herbicide glyphosate. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. Theses impacts may have played a major role in the decline in pheasant populations.


id: cord-335372-tncjfdtp
author: HACKNEY, RAYMOND W.
date: 1998-11-30
url: https://api.elsevier.com/content/article/pii/S000281771560112X
doi: 10.14219/jada.archive.1998.0103
title:
  USING A BIOLOGICAL INDICATOR TO DETECT POTENTIAL SOURCES OF CROSS-CONTAMINATION IN THE DENTAL OPERATORY

abstract:
  ABSTRACT The authors conducted a study using surveillance monitoring methodology to identify operatory contamination and to evaluate the effectiveness of infection control procedures. Viridans streptococci were evaluated as biological indicators of oral contamination. Viridans streptococci, abundant in human saliva, were detected on operatory surfaces after dental treatments were finished and surfaces were disinfected. The findings validate current concepts of infection control as demonstrated in barrier methods.


id: cord-335375-n6q70o35
author: Chan, Paul K. S.
date: 2005-07-01
txt: ./txt/cord-335375-n6q70o35.txt
cache: ./cache/cord-335375-n6q70o35.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15942907/
doi: 10.1086/430615
summary:
  Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner.

title:
  Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection

abstract:
  The maturation of virus-specific immunoglobulin G avidity during severe acute respiratory syndrome–associated coronavirus infection was examined. The avidity indices were low (mean ± SD, 30.8% ± 11.6%) among serum samples collected ⩽50 days after fever onset, intermediate (mean ± SD, 52.1% ± 14.1%) among samples collected between days 51 and 90, and high (mean ± SD, 78.1% ± 8.0%) among samples collected after day 90. Avidity indices of 40% and 55% could be considered as cutoff values for determination of recent (⩽50 days) and past (>65 days) infection, respectively. Measurement of antibody avidity can be used to differentiate primary infection from reexposure and to assess humoral responses to candidate vaccines


id: cord-336103-ufvq0ngl
title: Optimal sample pooling: an efficient tool against SARS-CoV-2
author: Sharma, R.
date: 2020-07-04
txt: ./txt/cord-336103-ufvq0ngl.txt
cache: ./cache/cord-336103-ufvq0ngl.txt
extension: .txt
mime: text/plain
url: http://medrxiv.org/cgi/content/short/2020.07.03.20145953v1?rss=1
doi: 10.1101/2020.07.03.20145953
summary:
  2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2

abstract:
  The SARS-CoV-2 pandemic situation has presented multiple imminent challenges to the nations around the globe. While health agencies around the world are exploring various options to contain the spread of this fatal viral infection, multiple strategies and guidelines are being issued to boost the fight against the disease. Identifying and isolating infected individuals at an early phase of the disease has been a very successful approach to stop the chain of transmission. But this approach faces a practical challenge of limited resources. Sample pooling solves this enigma by significantly improving the testing capacity and result turn around time while using no extra resources. However, the general sample pooling method also has the scope of significant improvements. This article describes a process to further optimize the resources with optimal sample pooling. This is a user-friendly technique, scalable on a national or international scale. A mathematical model has been built and validated for its performance using clinical data.


id: cord-342538-5bwsm290
title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing
author: Izquierdo Lara, R. W.
date: 2020-09-22
txt: ./txt/cord-342538-5bwsm290.txt
cache: ./cache/cord-342538-5bwsm290.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.09.21.20198838
doi: 10.1101/2020.09.21.20198838
summary:
  Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina).

abstract:
  The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community.


id: cord-344131-e7phs0jd
title: Section 4 Diagnostic and Therapeutic Procedures
author: Ford, Richard B.
date: 2012-12-31
txt: ./txt/cord-344131-e7phs0jd.txt
cache: ./cache/cord-344131-e7phs0jd.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/B9781437707984000049
doi: 10.1016/b978-1-4377-0798-4.00004-9
abstract: nan
summary:
  Before actually collecting and submitting a sample to a laboratory for bacterial culture, it is appropriate (whenever feasible to do so) to prepare, stain, and examine, under direct microscopy, exudates or fluid from the suspect material or tissue. Fine-needle aspiration, the use of needle and syringe to remove cells from normal and abnormal tissue, apply them to a glass slide, stain the smear, and review the results immediately is among the most useful, cost-effective procedures available in clinical practice. Do not remove the syringe from the tissue while maintaining negative pressure, because this can Enlargement of nucleus or nuclei larger than 10 nm Decreased nuclear/cytoplasmic ratio Multinucleation because of abnormal mitosis Abnormal or frequent mitosis Variations in size and shape of nuclei Increase in size and number of nucleoli Increased basophilia of cellular cytoplasm; increased RNA content Anisokaryosis or pleomorphism Multinucleated giant cells box 4-4 cytologic feAtuRes of mAlignAncy 4 result in the aspiration of significant amounts of blood from the skin, thereby significantly diluting the sample with peripheral blood.


id: cord-344627-w2efsshj
title: Human Bocavirus 2 in Children, South Korea
author: Han, Tae-Hee
date: 2009-10-17
txt: ./txt/cord-344627-w2efsshj.txt
cache: ./cache/cord-344627-w2efsshj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19861084/
doi: 10.3201/eid1510.090337
abstract: nan
summary:
  We looked for HBoV-2 in clinical samples from children with various diseases, including acute LRTIs, Kawasaki disease, Henoch-Schönlein purpura, and hepatitis. Of the 212 samples tested, the following viruses were detected: human respiratory syncytial virus ( HBoV-1 was not detected in the study population. Recent studies have detected HBoV-1 in serum samples of children with Kawasaki disease and of an immunocompromised child with hepatitis (7, 8) . However, neither HBoV-1 nor HBoV-2 was detected in the 172 serum samples from 61 patients with hepatitis, 12 with Kawasaki disease, 18 with Henoch-Schönlein purpura, and 81 healthy children. We demonstrated HBoV-2 DNA in the respiratory tract secretions of children with acute LRTIs. In most positive samples, the virus was found in addition to other respiratory viruses. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus


id: cord-345144-zvu22n8f
author: Compagnone, D.
date: 2007-12-31
url: https://www.sciencedirect.com/science/article/pii/S0166526X06490292
doi: 10.1016/s0166-526x(06)49029-2
title:
  Chapter 29 Rapid detection of organophosphates, Ochratoxin A, and Fusarium sp. in durum wheat via screen printed based electrochemical sensors

abstract:
  Publisher Summary Most of the inhibition bioassays or biosensors for organophosphate and carbamate pesticides are based on the amperometric detection of the enzymatic product of the reaction. Applications of amperometric biosensing strategies for pesticide detection in real or spiked food samples have been recently reported. Most of the applications have been developed for vegetable matrices. Different formats of biosensors have been used: disposable screenprinted choline oxidase biosensors using acetylcholinesterase (AChE) in solution were utilized to detect pesticides. Screen-printed sensor developed using photolithographic conducting copper track, graphite–epoxy composite, and either AChE or butirrylcholinesterase was also used in the analysis of spiked (paraoxon and carbofuran) samples of tap water and fruit juices at sub-nanomolar concentration. Additionally, the developed device, which consists of the hand-held potentiostat, the multiplexer for eight-channel control and a dedicated software, can be used to detect organophosphates pesticides, such as dichlorvos and pirimiphos methyl at contamination level below the maximum residue limit settled by the European Union and also amplified DNA of F. culmorum.


id: cord-345302-wbkfjz8r
author: Devaney, Ryan
date: 2016-10-04
txt: ./txt/cord-345302-wbkfjz8r.txt
cache: ./cache/cord-345302-wbkfjz8r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27215546/
doi: 10.1080/03079457.2016.1193123
summary:
  This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Of specific interest is the enteric viral population associated with RSS of which many RNA and DNA viruses have been implicated and co-infections of multiple viruses such as rotavirus, chicken astrovirus (CAstV), avian nephritis virus (ANV), and reoviruses have been detected in birds affected with RSS or with poor performance (Reynolds et al., 1986; Guy, 1998; Kang et al., 2012) . Other enteric pathogens associated with avian malabsorption diseases include reoviruses, parvoviruses, and members of the family Caliciviridae; many of which have also been observed in broiler chickens Smyth et al., 2007; Pantin-Jackwood et al., 2008 , Wolf et al., 2011 .

title:
  A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds

abstract:
  Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.


id: cord-345992-3ij1vbqp
title: SARS Molecular Detection External Quality Assurance
author: Drosten, Christian
date: 2004-12-17
url: https://www.ncbi.nlm.nih.gov/pubmed/15663861/
doi: 10.3201/eid1012.040416
abstract:
  Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Of 58 participants, 51 correctly detected virus in all samples >9,400 RNA copies per milliliter and none in negative samples. Commercial test kits significantly improved the outcome.


id: cord-346906-1wmp43ti
title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples
author: Lewandowski, Kuiama
date: 2019-12-23
txt: ./txt/cord-346906-1wmp43ti.txt
cache: ./cache/cord-346906-1wmp43ti.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1128/jcm.00963-19
doi: 10.1128/jcm.00963-19
summary:
  We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events.

abstract:
  Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 10(2) to 10(3) genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10(−5)). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [C(T)] values, <30) and 6/13 samples with low viral titers (C(T) values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.


id: cord-348464-1c08mb2k
author: Winter, Taylor
date: 2020-06-15
txt: ./txt/cord-348464-1c08mb2k.txt
cache: ./cache/cord-348464-1c08mb2k.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s11469-020-00342-9
doi: 10.1007/s11469-020-00342-9
summary:
  Consistent with the earlier validation studies, the FCV-19S displayed a moderately strong relationship with the perceived infectability and germ aversion subscales of the perceived vulnerability to disease scale (PVDS). With respect to the motivating role of fear, there was a significant relationship between FCV-19S scores and adherence to the lockdown rules that were implemented in New Zealand. Finally, consistent with recent reports on the politicization of the COVID-19 pandemic, an exploratory question found that participants who rated themselves as more conservative tended to report lower FCV-19S scores. The current study demonstrates that the English version of the COVID-19S is a sound unidimensional scale with robust psychometric properties that can be used with confidence Also shown is the association between FCV-19S and adherence to each rule among English-speaking populations. Validation and psychometric evaluation of the Italian version of the fear of COVID-19 scale

title:
  Evaluation of the English Version of the Fear of COVID-19 Scale and Its Relationship with Behavior Change and Political Beliefs

abstract:
  The COVID-19 pandemic has many individuals around the world fearing for their lives. The constant news coverage, rapid transmission, and relatively high mortality rate, make fearfulness a natural response. To assess the fear of COVID-19, the Fear of COVID-19 Scale (FCV-19S) was developed. The primary aim of the present study was to conduct the first psychometric assessment and validation of the English version of the FCV-19S. Two samples were collected in New Zealand. Sample 1 comprised 1624 participants of which 1397 completed all questions and were used in the analyses. Sample 2 comprised 1111 participants of which 1023 completed all questions and were used in the analyses. Several psychometric tests were conducted to ascertain the scale’s reliability and validity. Across both samples, the FCV-19S had high internal consistency. Consistent with the earlier validation studies, the FCV-19S displayed a moderately strong relationship with the perceived infectability and germ aversion subscales of the perceived vulnerability to disease scale (PVDS). Furthermore, FCV-19S scores were negatively correlated with the Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS) scores. With respect to the motivating role of fear, there was a significant relationship between FCV-19S scores and adherence to the lockdown rules that were implemented in New Zealand. Finally, consistent with recent reports on the politicization of the COVID-19 pandemic, an exploratory question found that participants who rated themselves as more conservative tended to report lower FCV-19S scores. The English version of the COVID-19S is a sound unidimensional scale with robust psychometric properties and can be used with confidence among English-speaking populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11469-020-00342-9) contains supplementary material, which is available to authorized users.


id: cord-353394-lq1f53qv
title: Detection of Pathogenic Viruses in the Ambient Air in Seoul, Korea
author: Han, Tae-Hee
date: 2018-05-14
url: https://www.ncbi.nlm.nih.gov/pubmed/29761411/
doi: 10.1007/s12560-018-9348-2
abstract:
  The possible transport of pathogenic microorganisms during Asian dust events could be an important concern for health workers; however, this is still uncertain owing to a lack of supporting evidence. The present study aimed to investigate the presence of pathogenic microorganisms in air samples collected during the Asian and non-Asian dust periods. Between March and September 2016, air samples were collected at three weather observation stations in Seoul using a high-volume air sampler. Multiplex PCR was performed using the Allplex™ respiratory and gastrointestinal panel assay kits to detect 46 microorganisms. RT-PCR was performed for klassevirus, Aichivirus, and human parechovirus (HPeV) detection. In total, 71 air samples were collected during the Asian (8 samples) and non-Asian (63 samples) dust events. During an Asian dust event, only one human rhinovirus (HRV)-positive air sample was collected on April 23. During the non-Asian dust period, HRV, HPeV, norovirus (NoV), enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), and Blastocystis hominis were detected in four, two, one, one, one, and one air samples, respectively. Pathogenic viruses were mostly detected in ambient air samples during the non-Asian dust period, which suggests a possible air-borne transmission of viral pathogens; however, the role of Asian dust in epidemics caused by pathogenic viruses is unclear.


id: cord-354372-vfvnjmv1
title: The autopsy at the time of SARS-CoV-2: Protocol and lessons
author: Carpenito, L.
date: 2020-07-04
url: https://www.ncbi.nlm.nih.gov/pubmed/32653819/
doi: 10.1016/j.anndiagpath.2020.151562
abstract:
  A new viral disease named COVID-19 has recently turned into a pandemic. Compared to a common viral pneumonia it may evolve in an atypical way, causing the rapid death of the patient. For over two centuries, autopsy has been recognized as a fundamental diagnostic technique, particularly for new or little-known diseases. To date, it is often considered obsolete giving the inadequacy to provide samples of a quality appropriate to the sophisticated diagnostic techniques available today. This is probably one of the reasons why during this pandemic autopsies were often requested only in few cases, late and discouraged, if not prohibited, by more than one nation. This is in contrast with our firm conviction: to understand the unknown we must look at it directly and with our own eyes. This has led us to implement an autopsy procedure that allows the beginning of the autopsy shortly after death (within 1–2 h) and its rapid execution, also including sampling for ultrastructural and molecular investigations. In our experience, the tissue sample collected for diagnosis and research were of quality similar to biopsy or surgical resections. This procedure was performed ensuring staff and environmental safety. We want to propose our experience, our main qualitative results and a few general considerations, hoping that they can be an incentive to use autopsy with a new procedure adjusted to match the diagnostic challenges of the third millennium.


id: cord-355351-seqwx9x1
title: Predicting geographic location from genetic variation with deep neural networks
author: Battey, CJ
date: 2020-06-08
txt: ./txt/cord-355351-seqwx9x1.txt
cache: ./cache/cord-355351-seqwx9x1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32511092/
doi: 10.7554/elife.54507
summary:
  At least in the context of windowed analyses, differences in predictions among windows appears to primarily reflect variation in ancestry rather than uncertainty in the inference itself, so we suggest the intervals returned by Locator''s kernel density estimation are best interpreted as representing areas from which a given proportion of the genome is likely to have originated. To test whether outlier geographic predictions reflect error in the model fitting procedure versus true variation in ancestry in a given region of the genome, we ran principal component analyses on windows for which a Maya individual (sample HGDP00871) has predicted locations in Europe and Africa. Test error was estimated as the distance in kilometers from the true sampling location to the geographic centroid of the cloud of per-window predictions, and is shown in Figure 8 plotted against local recombination rates from the HapMap genetic map (International HapMap Consortium, 2003) .

abstract:
  Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here, we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches. In simulations, Locator infers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverage Locator’s computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively.


id: cord-355743-vjiecd4k
title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing
author: Ghosh, Sabyasachi
date: 2020-04-29
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url: https://doi.org/10.1101/2020.04.23.20077727
doi: 10.1101/2020.04.23.20077727
summary:
  The decoding algorithm takes as input cycle threshold values from qPCR tests on the pools, and returns a result for each sample, along with an estimate of viral load if positive. Once pooled tests are run, the cycle threshold values can be entered into the app which solves for and displays the list of positive and negative samples along with an estimate of viral loads. 16 × 40 pooling matrix: Table 2 shows the emulated cycle threshold (Ct) values for the 16 RT-qPCR tests corresponding to five different trials (0, 1, 2, 3 or 4 positive samples out of a total of 40 samples). 24 × 60 pooling matrix: Table 3 shows the cycle threshold (Ct) values obtained for the 24 RT-qPCR tests corresponding to a trial with 2 positive samples out of a total of 60 samples.

abstract:
  The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We present Tapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android application BYOM Smart Testing which guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample.


